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Crystal Structure of a Cu-Zn Superoxide Dismutase from Mycobacterium tuberculosis at 1.63 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JCV PDB ENTRY 1JCV.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 4000, Ammonium sulfate, zinc chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal Properties Matthews coefficient Solvent content 2.03 39.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.04 α = 90 b = 58.42 β = 126.99 c = 51.39 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.9755 ESRF ID13
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 1.634 27.95 96 0.067 13.54 3.62 20248 20248 21.844
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 1.634 1.8 87.9 0.273 5.17 3.27 4640
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 PDB ENTRY 1JCV.pdb 1.63 27.95 20248 19233 1013 98.2 0.15233 0.15233 0.15029 0.1647 0.19027 0.1996 RANDOM 13.359
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] 0.82 1.19 -0.52 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.233 r_scangle_it 3.475 r_scbond_it 2.123 r_angle_other_deg 1.858 r_mcangle_it 1.484 r_angle_refined_deg 1.356 r_mcbond_it 0.831 r_symmetry_vdw_other 0.328 r_nbd_other 0.253 r_nbd_refined 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.233 r_scangle_it 3.475 r_scbond_it 2.123 r_angle_other_deg 1.858 r_mcangle_it 1.484 r_angle_refined_deg 1.356 r_mcbond_it 0.831 r_symmetry_vdw_other 0.328 r_nbd_other 0.253 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.132 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.01 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1204 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing