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Crystal Structure Analysis of MTB PEPCK mutant C273S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 0.1M Sodium acetate pH 4.6, 30% PEG 300
Crystal Properties Matthews coefficient Solvent content 2.92 57.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.721 α = 90 b = 124.598 β = 90 c = 121.302 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 120 IMAGE PLATE MAR scanner 345 mm plate 2014-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54
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 2.602 43.5 98.6 0.079 16.4 2.9 24105 2 57.22
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) 1 2.602 2.73 93.8 0.26 1.95 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4r43 2.602 43.46 22899 1206 98.67 0.19977 0.1974 0.24419 0.2056 RANDOM 45.614
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] -0.02 0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.363 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 6.399 r_long_range_B_refined 5.178 r_long_range_B_other 5.176 r_scangle_other 3.452 r_mcangle_it 3.314 r_mcangle_other 3.314 r_scbond_it 2.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.363 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 6.399 r_long_range_B_refined 5.178 r_long_range_B_other 5.176 r_scangle_other 3.452 r_mcangle_it 3.314 r_mcangle_other 3.314 r_scbond_it 2.098 r_scbond_other 2.098 r_mcbond_it 2.036 r_mcbond_other 2.034 r_angle_refined_deg 1.312 r_angle_other_deg 0.913 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4562 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing