2GW2

Crystal structure of the peptidyl-prolyl isomerase domain of human cyclophilin G


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52912M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9536.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.432α = 90
b = 65.504β = 90
c = 69.341γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.830900.1485.8414841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8656.40.632.2

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 1A581.829.6171460472889.1360.220.21680.2793Random14.14
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]
1.093-0.175-0.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.55
r_dihedral_angle_4_deg18.908
r_dihedral_angle_3_deg12.443
r_dihedral_angle_1_deg7.468
r_scangle_it3.592
r_mcangle_it3.264
r_scbond_it2.939
r_mcbond_it2.836
r_angle_refined_deg1.474
r_angle_other_deg0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.55
r_dihedral_angle_4_deg18.908
r_dihedral_angle_3_deg12.443
r_dihedral_angle_1_deg7.468
r_scangle_it3.592
r_mcangle_it3.264
r_scbond_it2.939
r_mcbond_it2.836
r_angle_refined_deg1.474
r_angle_other_deg0.981
r_mcbond_other0.928
r_symmetry_vdw_other0.238
r_nbd_other0.196
r_symmetry_vdw_refined0.186
r_nbd_refined0.18
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.124
r_symmetry_hbond_refined0.12
r_chiral_restr0.091
r_nbtor_other0.083
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1342
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction