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Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with inhibitor (surface entropy reduction mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277.15 22% PEG8000, 0.1M sodium cacodylate pH 5.0, 0.2M sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.53 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.01 α = 90 b = 119.523 β = 90 c = 145.753 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER2 X 16M 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 49.22 100 0.159 0.046 0.994 11.1 13 21451 47.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 1.202 0.355 0.924 1.4 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3IW0 2.3 37.7 1.38 21351 1109 99.7 0.1931 0.1912 0.1922 0.2263 0.2243 57.45
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 11.4697 f_angle_d 0.5697 f_chiral_restr 0.0379 f_plane_restr 0.0037 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3211 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing