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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 1.99 38.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.03 α = 90 b = 57.03 β = 90 c = 86.989 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 315r 2008-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 25.51 87.8 0.042 4.8 25100 23793 2.7 16.5
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 78 0.252 3.8
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 1.4 25.51 25100 23793 1290 86.58 0.15926 0.15777 0.1655 0.18727 0.1891 RANDOM 6.578
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.848 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 9.467 r_dihedral_angle_1_deg 5.997 r_scangle_it 1.077 r_angle_refined_deg 0.985 r_angle_other_deg 0.819 r_scbond_it 0.673 r_mcangle_it 0.502 r_mcbond_it 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.848 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 9.467 r_dihedral_angle_1_deg 5.997 r_scangle_it 1.077 r_angle_refined_deg 0.985 r_angle_other_deg 0.819 r_scbond_it 0.673 r_mcangle_it 0.502 r_mcbond_it 0.27 r_chiral_restr 0.063 r_mcbond_other 0.053 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 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 321 Heterogen Atoms 32
Software Software Software Name Purpose DNA data collection X-PLOR model building REFMAC refinement MOSFLM data reduction SCALA data scaling X-PLOR phasing