3RD9

Human Cyclophilin D Complexed with a Fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BITPDB ENTRY 2BIT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329130% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 100K, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
238.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.214α = 90
b = 57.214β = 90
c = 87.198γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.429.796.30.0497.1277582673129.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.43679.80.0818.42.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BIT1.429.662755826731141496.240.1230.123060.121690.14965RANDOM10.163
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]
0.10.1-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.517
r_dihedral_angle_4_deg15.398
r_dihedral_angle_3_deg10.091
r_dihedral_angle_1_deg6.191
r_angle_refined_deg1.193
r_scangle_it1.052
r_angle_other_deg0.826
r_scbond_it0.821
r_mcangle_it0.513
r_mcbond_it0.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.517
r_dihedral_angle_4_deg15.398
r_dihedral_angle_3_deg10.091
r_dihedral_angle_1_deg6.191
r_angle_refined_deg1.193
r_scangle_it1.052
r_angle_other_deg0.826
r_scbond_it0.821
r_mcangle_it0.513
r_mcbond_it0.382
r_nbd_refined0.184
r_nbd_other0.184
r_symmetry_vdw_refined0.176
r_nbtor_refined0.174
r_symmetry_vdw_other0.133
r_symmetry_hbond_refined0.113
r_xyhbond_nbd_refined0.105
r_mcbond_other0.093
r_nbtor_other0.086
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1240
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms24

Software

Software
Software NamePurpose
DNAdata collection
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing