2BIT

Crystal structure of human cyclophilin D at 1.7 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SWJPDB ENTRY 1SWJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1731 MG/ML PROTEIN, 50 MM NA-PHOSPHATE (PH 7.3), 100 MM NACL, 2MM EDTA, 30% JEFFAMINE
Crystal Properties
Matthews coefficientSolvent content
2.0138.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.165α = 90
b = 57.165β = 90
c = 87.227γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHOSMIC MIRRORS2001-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODENONIUS

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
11.711599.20.0520.85.691268
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)
11.711.8298.50.1410.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1SWJ1.71151531181199.40.1410.1390.175RANDOM14.14
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]
0.120.12-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.025
r_scangle_it2.202
r_scbond_it1.314
r_angle_refined_deg1.098
r_mcangle_it0.654
r_mcbond_it0.346
r_symmetry_vdw_refined0.217
r_symmetry_hbond_refined0.182
r_nbd_refined0.179
r_xyhbond_nbd_refined0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.025
r_scangle_it2.202
r_scbond_it1.314
r_angle_refined_deg1.098
r_mcangle_it0.654
r_mcbond_it0.346
r_symmetry_vdw_refined0.217
r_symmetry_hbond_refined0.182
r_nbd_refined0.179
r_xyhbond_nbd_refined0.11
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1240
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing