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Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6W PDB entry 2Z6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 291 30% Peg 4000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.927 α = 90 b = 57.927 β = 90 c = 88.537 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 315r 2010-07-25 M SINGLE WAVELENGTH 2 1 x-ray 298 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97964 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2 1.54 28.976 86.2 3.6 19640 18518
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.54 1.62 82.1 0.299 2.2 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION isomorphous THROUGHOUT PDB entry 2Z6W 1.54 27.53 2 19640 18518 982 86.2 0.151 0.14974 0.1476 0.1579 0.1894 0.1961 RANDOM 13.386
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.86 r_dihedral_angle_4_deg 15.77 r_dihedral_angle_3_deg 12.807 r_dihedral_angle_1_deg 5.79 r_scangle_it 3.209 r_scbond_it 2.185 r_mcangle_it 1.501 r_angle_refined_deg 1.23 r_mcbond_it 0.921 r_angle_other_deg 0.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.86 r_dihedral_angle_4_deg 15.77 r_dihedral_angle_3_deg 12.807 r_dihedral_angle_1_deg 5.79 r_scangle_it 3.209 r_scbond_it 2.185 r_mcangle_it 1.501 r_angle_refined_deg 1.23 r_mcbond_it 0.921 r_angle_other_deg 0.883 r_rigid_bond_restr 0.837 r_mcbond_other 0.245 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1230 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose DNA data collection REFMAC refinement MOSFLM data reduction SCALA data scaling