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1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inorganic pyrophosphatase (PPase) at pH5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 1.7 M ammonium sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.49 64.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.46 α = 90 b = 98.46 β = 90 c = 97.353 γ = 120
Symmetry Space Group P 63 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 120 CCD ADSC QUANTUM 4 mirrors 2004-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
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 1.3 84.5 99.2 0.063 0.063 32 8.2 68651 68086 2 2 14.7
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 1.3 1.32 98.2 0.683 0.683 3.15 7.2 3296
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 2PRD 1.3 84.5 2 64618 64618 3444 99.17 0.15514 0.15514 0.15437 0.1545 0.16945 0.1683 RANDOM 14.899
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] 0.63 0.32 0.63 -0.95
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 10.535 r_dihedral_angle_1_deg 6.303 r_sphericity_bonded 5.343 r_scangle_it 3.915 r_scbond_it 2.687 r_mcangle_it 2.043 r_angle_refined_deg 1.667 r_mcbond_it 1.396 r_angle_other_deg 1.077 r_rigid_bond_restr 0.811
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 10.535 r_dihedral_angle_1_deg 6.303 r_sphericity_bonded 5.343 r_scangle_it 3.915 r_scbond_it 2.687 r_mcangle_it 2.043 r_angle_refined_deg 1.667 r_mcbond_it 1.396 r_angle_other_deg 1.077 r_rigid_bond_restr 0.811 r_symmetry_vdw_other 0.333 r_nbd_other 0.26 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.097 r_nbtor_other 0.088 r_symmetry_vdw_refined 0.065 r_bond_refined_d 0.013 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1276 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing