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Crystal structure of inorganic pyrophosphatase from Staphylococcus aureus in complex with Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K23 PDB ID: 1K23, each domain individually, sequentially
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 1.32 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.3 71.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.406 α = 90 b = 99.406 β = 90 c = 425.285 γ = 120
Symmetry Space Group P 61 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 IMAGE PLATE MAR scanner 300 mm plate 2014-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.1 50 100 74109 74109 3 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ID: 1K23, each domain individually, sequentially 2.1 40 70192 70192 3695 99.93 0.22181 0.22037 0.2274 0.24922 0.2548 RANDOM 38.892
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] 1.03 0.52 1.03 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.602 r_dihedral_angle_3_deg 16.979 r_dihedral_angle_4_deg 9.09 r_dihedral_angle_1_deg 5.39 r_long_range_B_refined 4.653 r_long_range_B_other 4.402 r_scangle_other 2.251 r_mcangle_it 1.97 r_mcangle_other 1.97 r_scbond_it 1.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.602 r_dihedral_angle_3_deg 16.979 r_dihedral_angle_4_deg 9.09 r_dihedral_angle_1_deg 5.39 r_long_range_B_refined 4.653 r_long_range_B_other 4.402 r_scangle_other 2.251 r_mcangle_it 1.97 r_mcangle_other 1.97 r_scbond_it 1.334 r_scbond_other 1.331 r_mcbond_it 1.137 r_mcbond_other 1.137 r_angle_refined_deg 1.022 r_angle_other_deg 0.711 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 4760 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling