3QYU

Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z6WPDB entry 2Z6W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.329130% Peg 4000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.141.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.927α = 90
b = 57.927β = 90
c = 88.537γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 315r2010-07-25MSINGLE WAVELENGTH
21x-ray298MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97964ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1,21.5428.97686.23.61964018518
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)
1,21.541.6282.10.2992.22.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONisomorphousTHROUGHOUTPDB entry 2Z6W1.5427.532196401851898286.20.1510.149740.14760.1894RANDOM13.386
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.86
r_dihedral_angle_4_deg15.77
r_dihedral_angle_3_deg12.807
r_dihedral_angle_1_deg5.79
r_scangle_it3.209
r_scbond_it2.185
r_mcangle_it1.501
r_angle_refined_deg1.23
r_mcbond_it0.921
r_angle_other_deg0.883
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.86
r_dihedral_angle_4_deg15.77
r_dihedral_angle_3_deg12.807
r_dihedral_angle_1_deg5.79
r_scangle_it3.209
r_scbond_it2.185
r_mcangle_it1.501
r_angle_refined_deg1.23
r_mcbond_it0.921
r_angle_other_deg0.883
r_rigid_bond_restr0.837
r_mcbond_other0.245
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1230
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling