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Crystal structure of Rv3671c from M. tuberculosis H37Rv, Ser343Ala mutant, inactive form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K6Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1 M Tris-HCl, 2.1 M ammonium phosphate monobasic, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.603 α = 101.68 b = 44.207 β = 97.56 c = 53.356 γ = 105.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-10-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.002 APS 21-ID-D
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 2.1 50 95 0.064 22.6 2.1 19845 18853 3.8
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) 2.1 2.14 84.3 0.215 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3K6Z 2.1 40 19845 18853 1018 94.53 0.22909 0.22909 0.22654 0.2261 0.27628 0.2739 RANDOM 34.377
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] 0.7 0.5 1.89 0.21 1.06 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.662 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_4_deg 8.232 r_dihedral_angle_1_deg 4.433 r_angle_refined_deg 0.926 r_scangle_it 0.826 r_scbond_it 0.471 r_mcangle_it 0.41 r_nbtor_refined 0.297 r_mcbond_it 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.662 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_4_deg 8.232 r_dihedral_angle_1_deg 4.433 r_angle_refined_deg 0.926 r_scangle_it 0.826 r_scbond_it 0.471 r_mcangle_it 0.41 r_nbtor_refined 0.297 r_mcbond_it 0.279 r_nbd_refined 0.171 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.081 r_symmetry_hbond_refined 0.065 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2822 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing