4KML
Probing the N-terminal beta-sheet conversion in the crystal structure of the full-length human prion protein bound to a Nanobody
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2W9E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | A9 of the MD-proplex screen - 0.2 M sodium chloride, 0.1 M MES pH 6.0, 20% w/v PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.666723 | 26.202501 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 131.442 | α = 90 |
b = 45.921 | β = 96.09 |
c = 44.964 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 200 | CCD | MARMOSAIC 225 mm CCD | 2011-04-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.000 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 44.7 | 96.9 | 83742 | 42289 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.5 | 1.58 | 97.2 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2W9E | 1.5 | 31.61 | 40119 | 2112 | 98.46 | 0.17608 | 0.17523 | 0.18 | 0.19211 | 0.2 | RANDOM | 18.083 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.603 |
r_dihedral_angle_4_deg | 17.905 |
r_dihedral_angle_3_deg | 12.172 |
r_dihedral_angle_1_deg | 6.207 |
r_angle_refined_deg | 2.299 |
r_angle_other_deg | 0.973 |
r_chiral_restr | 0.146 |
r_bond_refined_d | 0.027 |
r_gen_planes_refined | 0.013 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1823 |
Nucleic Acid Atoms | |
Solvent Atoms | 89 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
SCALA | data scaling |