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Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2REQ PDB entry 2REQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM sodium cacodylate/HCl, pH 6.5, 800 mM sodium citrate tribasic dihydrate, 0.05% w/v casein, 0.05% w/v hemoglobin, 0.0005% w/v pepsin, 0.0005% w/v protease, 0.0005% w/v Proteinase K, 0.0005% w/v trypsin, 0.002 M HEPES sodium, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.802 α = 90 b = 103.561 β = 90 c = 211.197 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M K-B pair of biomorph mirrors for vertical and horizontal focusing 2018-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.9 29.1 96.5 0.126 0.16 0.993 7.9 4.1 129672 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 95.4 0.887 1.104 0.636 1.7 4
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 PDB entry 2REQ 1.9 28.967 1.33 129577 6579 96.12 0.1639 0.1618 0.1651 0.2019 0.2052
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 12.087 f_angle_d 1.244 f_chiral_restr 0.136 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10035 Nucleic Acid Atoms Solvent Atoms 1385 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing