☰ Navigation Tabs
Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with hexanoyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295.15 4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 4.02 69.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.488 α = 90 b = 276.488 β = 90 c = 390.12 γ = 90
Symmetry Space Group I 4 2 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 EIGER2 X 16M 2024-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953731 Diamond I04
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 1.95 225.58 100 0.233 0.045 0.999 12.6 27.4 538030
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 10.68 225.58 99.9 0.033 0.006 1 61.5 26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 225.579 537936 27053 99.981 0.206 0.2046 0.2155 0.2333 0.2425 39.016
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] 0.152 0.152 -0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.762 r_dihedral_angle_6_deg 14.476 r_dihedral_angle_2_deg 10.767 r_lrange_it 8.141 r_lrange_other 8.124 r_dihedral_angle_1_deg 7.003 r_scangle_it 6.475 r_scangle_other 6.475 r_mcangle_it 5.726 r_mcangle_other 5.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.762 r_dihedral_angle_6_deg 14.476 r_dihedral_angle_2_deg 10.767 r_lrange_it 8.141 r_lrange_other 8.124 r_dihedral_angle_1_deg 7.003 r_scangle_it 6.475 r_scangle_other 6.475 r_mcangle_it 5.726 r_mcangle_other 5.726 r_dihedral_angle_other_2_deg 5.53 r_scbond_it 4.42 r_scbond_other 4.42 r_mcbond_it 4.036 r_mcbond_other 4.034 r_angle_refined_deg 1.884 r_angle_other_deg 0.607 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.225 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.181 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_other 0.127 r_symmetry_xyhbond_nbd_refined 0.119 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32548 Nucleic Acid Atoms Solvent Atoms 2235 Heterogen Atoms 660
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building