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Structure of CypD in complex with an inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 4M potassium formate, 0.1M BIS-TRIS propane pH 9, 2% w/v PEG2000
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.131 α = 90 b = 57.131 β = 90 c = 117.774 γ = 90
Symmetry Space Group P 43 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 EIGER R 4M 2018-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.25 41 98 0.997 13.9 6.5 9525 26.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 99 0.837
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 38.21 1.35 9507 483 96.82 0.1617 0.1603 0.1628 0.1848 0.1875 26.98
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 8.6761 f_angle_d 0.7939 f_chiral_restr 0.052 f_plane_restr 0.0069 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing