2HQ6
Structure of the Cyclophilin_CeCYP16-Like Domain of the Serologically Defined Colon Cancer Antigen 10 from Homo Sapiens
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZKC | pdb entry 1ZKC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 298 | Protein is 20 mg/mL, in buffer containing 50 mM Tris pH 8.0, 500 mM NaCl, 5 mM BME; hanging drop, 1+1; precipitant is 20% Peg 3350, 0.2M NaI (no buffer); cryo was 20% glycerol, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.433 | α = 90 |
b = 84.433 | β = 90 |
c = 55.289 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | IMAGE PLATE | RIGAKU RAXIS IV | 2006-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.54178 |
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 | 1.75 | 24.7 | 98.5 | 0.136 | 9.2 | 3.2 | 22463 | 22463 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 1.75 | 1.81 | 98.2 | 0.61 | 2.3 | 3.2 | 2241 |
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 (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 | pdb entry 1ZKC | 1.75 | 24.7 | 22773 | 21296 | 1162 | 98.62 | 0.16744 | 0.16671 | 0.18 | 0.18093 | 0.2 | RANDOM | 25.198 |
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] | |
0.65 | 0.33 | 0.65 | -0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.863 |
r_dihedral_angle_4_deg | 15.968 |
r_dihedral_angle_3_deg | 12.128 |
r_dihedral_angle_1_deg | 6.167 |
r_scangle_it | 3.595 |
r_scbond_it | 2.368 |
r_angle_refined_deg | 1.538 |
r_mcangle_it | 1.289 |
r_mcbond_it | 0.855 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1333 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
ARP/wARP | model building |