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Human Cyclophilin D Complexed with a Fragment
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 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.379 α = 90 b = 57.379 β = 90 c = 87.784 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 ID14-2 ESRF ID14-2
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 1.1 36.835 84.3 0.089 8 50416 47849 3.5 15.1
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 1.1 1.129 82.3 0.563 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.1 36.83 50416 47849 2510 83.73 0.13523 0.13433 0.1436 0.15269 0.1592 RANDOM 5.576
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] 0.08 0.08 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 9.995 r_dihedral_angle_1_deg 6.209 r_angle_refined_deg 1.099 r_angle_other_deg 0.827 r_mcbond_it 0.532 r_nbd_refined 0.195 r_nbd_other 0.187 r_nbtor_refined 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 9.995 r_dihedral_angle_1_deg 6.209 r_angle_refined_deg 1.099 r_angle_other_deg 0.827 r_mcbond_it 0.532 r_nbd_refined 0.195 r_nbd_other 0.187 r_nbtor_refined 0.18 r_mcbond_other 0.16 r_symmetry_vdw_other 0.14 r_xyhbond_nbd_refined 0.088 r_nbtor_other 0.084 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.073 r_symmetry_vdw_refined 0.036 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 10
Software Software Software Name Purpose DNA data collection X-PLOR model building REFMAC refinement MOSFLM data reduction SCALA data scaling X-PLOR phasing