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Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 6 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 7.75
1.4 M K H2PO4
2 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 3.55 65.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.972 α = 90 b = 98.972 β = 90 c = 97.571 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 2015-12-19 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 2.45 50 97.7 29 11.8 10662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 99.8 12.2
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 2.45 50 10141 520 97.83 0.18798 0.18644 0.193 0.21763 0.2259 RANDOM 45.756
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] 0.02 0.01 0.02 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.47 r_dihedral_angle_3_deg 15.495 r_dihedral_angle_4_deg 12.047 r_long_range_B_refined 7.379 r_long_range_B_other 7.295 r_dihedral_angle_1_deg 6.472 r_scangle_other 4.793 r_mcangle_it 3.755 r_mcangle_other 3.753 r_scbond_it 2.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.47 r_dihedral_angle_3_deg 15.495 r_dihedral_angle_4_deg 12.047 r_long_range_B_refined 7.379 r_long_range_B_other 7.295 r_dihedral_angle_1_deg 6.472 r_scangle_other 4.793 r_mcangle_it 3.755 r_mcangle_other 3.753 r_scbond_it 2.894 r_scbond_other 2.814 r_mcbond_it 2.568 r_mcbond_other 2.322 r_angle_refined_deg 1.62 r_angle_other_deg 0.908 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 27 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing