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Crystal structure of 6-phosphogluconolactonase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 JCSG condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350, 26.9 mg/mL protein, Crystal Tracking ID 202955h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.301 α = 108.5 b = 68.081 β = 107.11 c = 73.542 γ = 104.95
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 RIGAKU SATURN 944+ 2009-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.15 50 95.6 0.056 23.75 4 48256
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 2.15 2.23 90.8 0.178 7.4 3.8 4584
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VL1 2.15 33.9 48228 2412 95.43 0.184 0.182 0.1853 0.223 0.1878 RANDOM 19.629
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] 0.61 1.06 -0.39 0.41 0.05 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.008 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 15.203 r_dihedral_angle_1_deg 5.979 r_scangle_it 2.749 r_scbond_it 1.615 r_angle_refined_deg 1.268 r_mcangle_it 0.943 r_mcbond_it 0.502 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.008 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 15.203 r_dihedral_angle_1_deg 5.979 r_scangle_it 2.749 r_scbond_it 1.615 r_angle_refined_deg 1.268 r_mcangle_it 0.943 r_mcbond_it 0.502 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7208 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling