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Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with Ca ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 GROWN IN 9% PEG 4,000, 100 MM HEPES PH
7.0 AND 100 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
295K
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.118 α = 90 b = 102.118 β = 90 c = 80.426 γ = 120
Symmetry Space Group P 32 2 1
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 1.95 32 100 44.2 12.4 33886
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 4JQQ 1.95 31.59 33886 1788 100 0.209 0.206 0.2088 0.254 0.2504 RANDOM 32.85
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.481 r_dihedral_angle_4_deg 14.697 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 5.947 r_angle_other_deg 1.927 r_angle_refined_deg 1.324 r_chiral_restr 0.088 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.481 r_dihedral_angle_4_deg 14.697 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 5.947 r_angle_other_deg 1.927 r_angle_refined_deg 1.324 r_chiral_restr 0.088 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3854 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 3
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling