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Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with two phosphate ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 reservoir: 1.6 M KH2PO4, 100 mM HEPES pH 7.75 and 2 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 3.54 65.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.319 α = 90 b = 99.319 β = 90 c = 96.732 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 100 CCD MARMOSAIC 225 mm CCD 2014-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97872 APS 22-ID
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 2.35 50 99.3 18.1 7.1 11538
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 4Z71 2.352 40 11538 606 99.39 0.20965 0.20806 0.2118 0.24094 0.2384 RANDOM 39.437
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] 0.53 0.26 0.53 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.683 r_dihedral_angle_3_deg 14.014 r_dihedral_angle_4_deg 13.223 r_dihedral_angle_1_deg 5.898 r_long_range_B_refined 5.383 r_long_range_B_other 5.196 r_scangle_other 3.359 r_mcangle_it 2.607 r_mcangle_other 2.606 r_scbond_it 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.683 r_dihedral_angle_3_deg 14.014 r_dihedral_angle_4_deg 13.223 r_dihedral_angle_1_deg 5.898 r_long_range_B_refined 5.383 r_long_range_B_other 5.196 r_scangle_other 3.359 r_mcangle_it 2.607 r_mcangle_other 2.606 r_scbond_it 2.097 r_scbond_other 2.088 r_mcbond_it 2.038 r_mcbond_other 1.654 r_angle_refined_deg 1.492 r_angle_other_deg 0.728 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1278 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing