3RCF

Human cyclophilin D complexed with N-[(4-aminophenyl)sulfonyl]benzamide


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 291K
Crystal Properties
Matthews coefficientSolvent content
2.0339.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.518α = 90
b = 57.518β = 90
c = 87.564γ = 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 ID14-2ESRFID14-2

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
11.1527.398.20.0657.3502524924719.919.9
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)
11.151.1890.90.2636.3

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 2BIT1.1526.035025249247258398.060.1260.12640.125160.15RANDOM5.305
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.275
r_dihedral_angle_4_deg15.075
r_dihedral_angle_3_deg10.334
r_dihedral_angle_1_deg5.958
r_sphericity_free1.979
r_scangle_it1.295
r_angle_refined_deg1.164
r_sphericity_bonded1.097
r_scbond_it1.033
r_mcangle_it0.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.275
r_dihedral_angle_4_deg15.075
r_dihedral_angle_3_deg10.334
r_dihedral_angle_1_deg5.958
r_sphericity_free1.979
r_scangle_it1.295
r_angle_refined_deg1.164
r_sphericity_bonded1.097
r_scbond_it1.033
r_mcangle_it0.856
r_angle_other_deg0.826
r_mcbond_it0.588
r_rigid_bond_restr0.456
r_nbd_refined0.223
r_mcbond_other0.202
r_nbd_other0.189
r_symmetry_vdw_other0.189
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.127
r_nbtor_other0.085
r_symmetry_hbond_refined0.079
r_chiral_restr0.075
r_symmetry_vdw_refined0.074
r_bond_refined_d0.006
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1237
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms38

Software

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