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0.85A resolution structure of PEG 400 Bound Cyclophilin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 25% (w/v) PEG 4000, 100 mM Hepes, 200 NaCl, pH 7.5, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.02 α = 90 b = 57.02 β = 90 c = 87.159 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 PIXEL DECTRIS PILATUS 6M 2013-01-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 0.85 47.72 97.7 0.049 30.7 14.2 123449 123449 -3 6.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.85 0.86 60.2 0.342 1.8 1.7 3694
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2BIT 0.85 28.51 1.1 123339 123339 6189 97.71 0.1077 0.1071 0.1195 0.1188 0.1315 RANDOM 7.9686
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.096 f_angle_d 1.482 f_chiral_restr 0.105 f_bond_d 0.015 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1232 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 23
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction JDirector data collection XSCALE data scaling