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2.1 A X-ray structure of CysM (Rv1336) from Mycobacterium tuberculosis an O-phosphoserine dependent cysteine synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q3B PDB ENTRY 2Q3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.423 α = 90 b = 89.222 β = 90 c = 98.766 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 110 CCD ADSC QUANTUM 315 Channel cut ESRF monochromator, Torodial focusing mirror 2008-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93400 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 98.8 0.071 0.085 13.9 3.1 38897 38431 2.6 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 99.7 0.453 0.539 2.6 3.2 5613
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 PDB ENTRY 2Q3B 2.1 28.58 2.6 37136 36490 1898 98.26 0.191 0.19343 0.19088 0.2081 0.24147 0.2534 RANDOM 23.102
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] 0.27 -1.1 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.112 r_dihedral_angle_3_deg 15.845 r_dihedral_angle_4_deg 14.248 r_dihedral_angle_1_deg 5.851 r_scangle_it 3.236 r_scbond_it 2.029 r_angle_refined_deg 1.398 r_mcangle_it 1.275 r_angle_other_deg 0.957 r_mcbond_it 0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.112 r_dihedral_angle_3_deg 15.845 r_dihedral_angle_4_deg 14.248 r_dihedral_angle_1_deg 5.851 r_scangle_it 3.236 r_scbond_it 2.029 r_angle_refined_deg 1.398 r_mcangle_it 1.275 r_angle_other_deg 0.957 r_mcbond_it 0.682 r_symmetry_hbond_refined 0.315 r_symmetry_vdw_other 0.28 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.213 r_nbd_other 0.2 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.172 r_mcbond_other 0.138 r_nbtor_other 0.086 r_metal_ion_refined 0.086 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4567 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection MOSFLM data reduction SCALA data scaling MOLREP phasing