3KIJ
Crystal structure of the human PDI-peroxidase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GS3 | PDB entry 2gs3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 295.15 | 2.5M ammonium sulfate, 0.1M 2-(N-morpholino)ethanesulfonic acid, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.43 | α = 90 |
b = 122.3 | β = 117.9 |
c = 70.18 | 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2006-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | 0.89997 | EMBL/DESY, HAMBURG | X12 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.8 | 66.9 | 99.3 | 0.071 | 16 | 5 | 61998 | 20.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.8 | 1.846 | 99.3 | 0.26 | 5.7 | 5.1 | 9242 |
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 | Phaser_MR | THROUGHOUT | PDB entry 2gs3 | 1.8 | 20 | 58897 | 3100 | 99.67 | 0.21059 | 0.2086 | 0.24811 | RANDOM | 16.184 |
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] | |
0.67 | 0.62 | -0.17 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.533 |
r_dihedral_angle_3_deg | 14.724 |
r_dihedral_angle_4_deg | 14.408 |
r_dihedral_angle_1_deg | 5.99 |
r_scangle_it | 3.621 |
r_scbond_it | 2.225 |
r_mcangle_it | 1.414 |
r_angle_refined_deg | 1.352 |
r_mcbond_it | 0.809 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4181 |
Nucleic Acid Atoms | |
Solvent Atoms | 517 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |