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Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 100 mM MES pH 6.5, 5% (v/v) PEG 400, 2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.04 59.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.197 α = 89.95 b = 57.286 β = 83.81 c = 75.274 γ = 89.86
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 Bruker Platinum 135 2012-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.39 45.47 90.94 7.82 3.22 30008 33.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 in-house structure 2.39 30.3 29998 1517 90.94 0.1978 0.1961 0.2106 0.2298 0.2458 RANDOM 19.55
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] -0.1115 -0.4018 1.2694 -2.0381 -0.9374 2.1496
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.98 t_omega_torsion 2.83 t_angle_deg 1.1 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.98 t_omega_torsion 2.83 t_angle_deg 1.1 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4976 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 1376
Software Software Software Name Purpose BUSTER refinement