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Determination of the crystal structure of the pyrazinamidase from M.tuberculosis : a structure-function analysis for prediction resistance to pyrazinamide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 298 1.6M Sulfate de Magnesium, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.1 α = 90 b = 84.1 β = 90 c = 100 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 CCD MARRESEARCH 2008-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.97 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 42.3 92.9 11.6 11014
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.3 72.5 0.498 3.4 11.5 1260
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 1IM5 2.2 42.03 10463 551 100 0.19679 0.1945 0.2014 0.23996 0.2439 RANDOM 45.08
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] 0.25 0.12 0.25 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.041 r_dihedral_angle_4_deg 24.402 r_dihedral_angle_3_deg 15.885 r_dihedral_angle_1_deg 9.182 r_scangle_it 5.698 r_scbond_it 3.829 r_mcangle_it 2.235 r_angle_refined_deg 2.118 r_mcbond_it 1.383 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.041 r_dihedral_angle_4_deg 24.402 r_dihedral_angle_3_deg 15.885 r_dihedral_angle_1_deg 9.182 r_scangle_it 5.698 r_scbond_it 3.829 r_mcangle_it 2.235 r_angle_refined_deg 2.118 r_mcbond_it 1.383 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.31 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.16 r_symmetry_vdw_refined 0.15 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 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 1372 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 1
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling