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Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inorganic pyrophosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 reservoir: 1.65 M NaKHPO4, 100 mM HEPES pH 7.75 and 2 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.011 α = 90 b = 105.199 β = 90 c = 255.872 γ = 90
Symmetry Space Group P 21 21 21
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 2012-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F
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 2.55 50 100 28.5 7.5 73541
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.55 35 73541 3890 99.94 0.2105 0.20842 0.2125 0.24943 0.2508 RANDOM 41.786
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] 2.44 -0.76 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.237 r_dihedral_angle_4_deg 15.29 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_1_deg 5.658 r_long_range_B_refined 3.299 r_long_range_B_other 3.297 r_mcangle_it 1.644 r_mcangle_other 1.644 r_angle_refined_deg 1.185 r_scangle_other 1.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.237 r_dihedral_angle_4_deg 15.29 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_1_deg 5.658 r_long_range_B_refined 3.299 r_long_range_B_other 3.297 r_mcangle_it 1.644 r_mcangle_other 1.644 r_angle_refined_deg 1.185 r_scangle_other 1.046 r_mcbond_it 0.938 r_mcbond_other 0.938 r_angle_other_deg 0.864 r_scbond_it 0.703 r_scbond_other 0.702 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_bond_other_d 0.006 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 15346 Nucleic Acid Atoms Solvent Atoms 883 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing