3RCI

Human cyclophilin D complexed with 5-methyl-1,2-oxazol-3-amine


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
238.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.154α = 90
b = 57.154β = 90
c = 87.657γ = 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
11.442999.90.067525620255959.7
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)
11.441.4799.60.4911.85.2

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 2BIT1.4426.022562025595136099.830.1690.169240.167770.19703RANDOM6.837
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]
-0.13-0.130.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.454
r_dihedral_angle_4_deg19.897
r_dihedral_angle_3_deg10.302
r_dihedral_angle_1_deg6.084
r_scangle_it2.018
r_angle_refined_deg1.392
r_scbond_it1.356
r_mcangle_it0.949
r_angle_other_deg0.845
r_mcbond_it0.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.454
r_dihedral_angle_4_deg19.897
r_dihedral_angle_3_deg10.302
r_dihedral_angle_1_deg6.084
r_scangle_it2.018
r_angle_refined_deg1.392
r_scbond_it1.356
r_mcangle_it0.949
r_angle_other_deg0.845
r_mcbond_it0.594
r_mcbond_other0.182
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1226
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms28

Software

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