2IGW
CYCLOPHILIN 3 complexed with DIPEPTIDE GLY-PRO
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E8K | PDB ENTRY 1E8K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 291 | 30% MPEG 5000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.25 | 61.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.724 | α = 90 |
b = 62.724 | β = 90 |
c = 122.756 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | EMBL/DESY, HAMBURG | BW7A |
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 | 1.78 | 36.04 | 98 | 0.123 | 11.7 | 4.3 | 23790 | 25.8 |
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) | |||||||||||
1.78 | 1.88 | 90.9 | 0.01424 | 0.9 | 4.2 | 3131 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | PDB ENTRY 1E8K | 1.78 | 35.95 | 23642 | 22427 | 1215 | 92.6 | 0.2245 | 0.2245 | 0.2245 | 0.2637 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
7 | 1436.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.075 |
s_anti_bump_dis_restr | 0.05 |
s_non_zero_chiral_vol | 0.037 |
s_zero_chiral_vol | 0.032 |
s_from_restr_planes | 0.0266 |
s_angle_d | 0.023 |
s_bond_d | 0.007 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1303 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
MAR345dtb | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |