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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, asp13asn mutant complexed with magnesium and tartrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QU2 PDB ENTRY 3QU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 0.1M POTASSIUM SODIUM TARTRATE, PH 8.0, 100MM IMIDAZOLE, 200MM SODIUM CHLORIDE, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 3.04 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.174 α = 90 b = 84.174 β = 90 c = 79.365 γ = 120
Symmetry Space Group P 31 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 90 CCD ADSC QUANTUM 315 MIRRORS 2009-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.87 40 99.1 0.069 8.1 6.7 27292 -5 37.927
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 1.87 1.94 92.8 0.82 1 4.1
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 PDB ENTRY 3QU2 1.9 20 25026 826 99.42 0.21028 0.20899 0.207 0.25249 0.2491 RANDOM 51.394
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] 2.02 1.01 2.02 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.129 r_dihedral_angle_4_deg 20.657 r_dihedral_angle_3_deg 16.124 r_scangle_it 12.284 r_scbond_it 9.354 r_mcangle_it 7.766 r_mcbond_it 6.081 r_dihedral_angle_1_deg 5.637 r_angle_refined_deg 1.352 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.129 r_dihedral_angle_4_deg 20.657 r_dihedral_angle_3_deg 16.124 r_scangle_it 12.284 r_scbond_it 9.354 r_mcangle_it 7.766 r_mcbond_it 6.081 r_dihedral_angle_1_deg 5.637 r_angle_refined_deg 1.352 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.223 r_xyhbond_nbd_refined 0.173 r_nbd_refined 0.169 r_symmetry_vdw_refined 0.164 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 18
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling