3MIB
Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound nitrite
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PHM | PDB ENTRY 1PHM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | Crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. Then, soaking in mother liquor supplemented with 300mM NaNO2 for 20 hours at 293K., VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.612 | α = 90 |
b = 68.617 | β = 90 |
c = 80.254 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2007-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.00 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.35 | 52 | 99.7 | 0.046 | 49.4 | 7.1 | 16345 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.35 | 2.43 | 100 | 0.49 | 3.7 | 6.8 | 1607 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1PHM | 2.35 | 52 | 15441 | 821 | 99.41 | 0.20201 | 0.19986 | 0.2444 | RANDOM | 61.863 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.6 | -3.28 | 2.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.8 |
r_dihedral_angle_4_deg | 17.174 |
r_dihedral_angle_3_deg | 13.856 |
r_dihedral_angle_1_deg | 6.145 |
r_scangle_it | 1.388 |
r_angle_refined_deg | 1.056 |
r_scbond_it | 0.991 |
r_mcangle_it | 0.612 |
r_mcbond_it | 0.366 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2399 |
Nucleic Acid Atoms | |
Solvent Atoms | 168 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |