3RCL

Human Cyclophilin D Complexed with a Fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329130% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthew coefficientSolvent content
1.9938.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.055α = 90
b = 57.055β = 90
c = 87.459γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMARRESEARCH2008-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
11.72298.10.025.915630153335.9
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)
11.71.74987.40.0373.73.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BIT1.721.86156301533379998.490.133630.131810.16936RANDOM5.838
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.977
r_dihedral_angle_4_deg21.177
r_dihedral_angle_3_deg12.272
r_dihedral_angle_1_deg5.925
r_scangle_it1.275
r_angle_refined_deg1.043
r_angle_other_deg0.891
r_scbond_it0.76
r_mcangle_it0.477
r_mcbond_it0.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.977
r_dihedral_angle_4_deg21.177
r_dihedral_angle_3_deg12.272
r_dihedral_angle_1_deg5.925
r_scangle_it1.275
r_angle_refined_deg1.043
r_angle_other_deg0.891
r_scbond_it0.76
r_mcangle_it0.477
r_mcbond_it0.264
r_chiral_restr0.065
r_mcbond_other0.056
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1240
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms34

Software

Software
Software NamePurpose
MAR345dtbdata collection
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing