3MIH

Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide, obtained in the presence of substrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PHMPDB ENTRY 1PHM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293Crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 1mM substrate (Ac-3,5-diI-YG) for 1 hour and then soaked in 40mM NaN3/1mM substrate for 8 hours at 293K., VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6753.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.11α = 90
b = 68.8β = 90
c = 79.791γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.98NSLSX4C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.745287.30.08921.14.88970-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.752.8549.30.411.73502

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PHM2.7452850242986.910.239940.237180.29587RANDOM84.396
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.13-3.42.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.382
r_dihedral_angle_3_deg14.214
r_dihedral_angle_4_deg13.222
r_dihedral_angle_1_deg5.473
r_angle_refined_deg0.967
r_scangle_it0.72
r_scbond_it0.429
r_nbtor_refined0.302
r_mcangle_it0.275
r_nbd_refined0.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.382
r_dihedral_angle_3_deg14.214
r_dihedral_angle_4_deg13.222
r_dihedral_angle_1_deg5.473
r_angle_refined_deg0.967
r_scangle_it0.72
r_scbond_it0.429
r_nbtor_refined0.302
r_mcangle_it0.275
r_nbd_refined0.172
r_symmetry_hbond_refined0.162
r_mcbond_it0.143
r_symmetry_vdw_refined0.138
r_xyhbond_nbd_refined0.099
r_metal_ion_refined0.075
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2393
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms26

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling