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Human Cyclophilin D Complexed with a Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIT PDB ENTRY 2BIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 291 30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.99 38.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.055 α = 90 b = 57.055 β = 90 c = 87.459 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 100 AREA DETECTOR MARRESEARCH 2008-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.7 22 98.1 0.02 5.9 15630 15333 5.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.749 87.4 0.037 3.7 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BIT 1.7 21.86 15630 15333 799 98.49 0.13363 0.13181 0.1414 0.16936 0.177 RANDOM 5.838
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.977 r_dihedral_angle_4_deg 21.177 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_1_deg 5.925 r_scangle_it 1.275 r_angle_refined_deg 1.043 r_angle_other_deg 0.891 r_scbond_it 0.76 r_mcangle_it 0.477 r_mcbond_it 0.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.977 r_dihedral_angle_4_deg 21.177 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_1_deg 5.925 r_scangle_it 1.275 r_angle_refined_deg 1.043 r_angle_other_deg 0.891 r_scbond_it 0.76 r_mcangle_it 0.477 r_mcbond_it 0.264 r_chiral_restr 0.065 r_mcbond_other 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 34
Software Software Software Name Purpose MAR345dtb data collection X-PLOR model building REFMAC refinement MOSFLM data reduction SCALA data scaling X-PLOR phasing