6R9X

Human Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-ylmethyl-oxalamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4J5B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1542.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.239α = 90
b = 57.239β = 90
c = 87.603γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.6687.694.60.06815.513.61683811.14
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)
11.661.9191.40.1953.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4J5B1.6615.3816793169594.90.1490.1440.193RANDOM10.54
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]
0.3720.372-0.744
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.65
t_omega_torsion4.27
t_angle_deg1.04
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.65
t_omega_torsion4.27
t_angle_deg1.04
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms18

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing