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Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 1 and inorganic pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.1 M HEPES pH 7.5, 1.6 M NaH2PO4, and 0.2 M KH2PO4
Crystal Properties Matthews coefficient Solvent content 3.62 65.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.965 α = 90 b = 99.965 β = 90 c = 97.559 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 RAYONIX MX300-HS 2015-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 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 2.65 50 99.6 29 6.8 8828
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 2.65 2.72 100 0.09 5 7.3
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 4Z72 2.65 50 8404 424 99.59 0.20578 0.20399 0.2125 0.24015 0.2344 RANDOM 57.261
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] 1.01 0.51 1.01 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.047 r_dihedral_angle_3_deg 14.988 r_dihedral_angle_4_deg 9.937 r_dihedral_angle_1_deg 5.515 r_long_range_B_other 3.722 r_long_range_B_refined 3.721 r_mcangle_it 2.237 r_mcangle_other 2.237 r_scangle_other 1.84 r_angle_refined_deg 1.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.047 r_dihedral_angle_3_deg 14.988 r_dihedral_angle_4_deg 9.937 r_dihedral_angle_1_deg 5.515 r_long_range_B_other 3.722 r_long_range_B_refined 3.721 r_mcangle_it 2.237 r_mcangle_other 2.237 r_scangle_other 1.84 r_angle_refined_deg 1.807 r_mcbond_it 1.225 r_mcbond_other 1.225 r_angle_other_deg 1.075 r_scbond_it 0.987 r_scbond_other 0.982 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 1282 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing