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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 100K, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.214 α = 90 b = 57.214 β = 90 c = 87.198 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 CCD ADSC QUANTUM 4 2007-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.4 29.7 96.3 0.049 7.1 27758 26731 29.4
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 1.4 1.436 79.8 0.081 8.4 2.4
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BIT 1.4 29.66 27558 26731 1414 96.24 0.123 0.12306 0.12169 0.1358 0.14965 0.1614 RANDOM 10.163
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] 0.1 0.1 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.517 r_dihedral_angle_4_deg 15.398 r_dihedral_angle_3_deg 10.091 r_dihedral_angle_1_deg 6.191 r_angle_refined_deg 1.193 r_scangle_it 1.052 r_angle_other_deg 0.826 r_scbond_it 0.821 r_mcangle_it 0.513 r_mcbond_it 0.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.517 r_dihedral_angle_4_deg 15.398 r_dihedral_angle_3_deg 10.091 r_dihedral_angle_1_deg 6.191 r_angle_refined_deg 1.193 r_scangle_it 1.052 r_angle_other_deg 0.826 r_scbond_it 0.821 r_mcangle_it 0.513 r_mcbond_it 0.382 r_nbd_refined 0.184 r_nbd_other 0.184 r_symmetry_vdw_refined 0.176 r_nbtor_refined 0.174 r_symmetry_vdw_other 0.133 r_symmetry_hbond_refined 0.113 r_xyhbond_nbd_refined 0.105 r_mcbond_other 0.093 r_nbtor_other 0.086 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 24
Software Software Software Name Purpose DNA data collection X-PLOR model building REFMAC refinement MOSFLM data reduction SCALA data scaling X-PLOR phasing