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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, asp13asn mutant complexed with calcium and phosphate
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 4.5 294 0.1M SODIUM ACETATE, PH 4.5, 30% PEG400, 200MM CALCIUM ACETATE, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.549 α = 90 b = 136.865 β = 90 c = 114.834 γ = 90
Symmetry Space Group C 2 2 21
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 2009-11-10 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 1.9 50 99.8 0.053 7.7 6.1 45325 -5
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 1.9 2 99.5 0.68 2 5.7
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 43820 1408 99.8 0.191 0.19 0.1889 0.226 0.2199 RANDOM 47.8
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] 2.1 -3.09 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.598 r_dihedral_angle_4_deg 21.828 r_dihedral_angle_3_deg 14.826 r_scangle_it 8.414 r_scbond_it 6.116 r_dihedral_angle_1_deg 5.385 r_mcangle_it 5.334 r_mcbond_it 4.083 r_angle_refined_deg 1.202 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.598 r_dihedral_angle_4_deg 21.828 r_dihedral_angle_3_deg 14.826 r_scangle_it 8.414 r_scbond_it 6.116 r_dihedral_angle_1_deg 5.385 r_mcangle_it 5.334 r_mcbond_it 4.083 r_angle_refined_deg 1.202 r_nbtor_refined 0.294 r_symmetry_hbond_refined 0.174 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.156 r_metal_ion_refined 0.149 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_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 3469 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 17
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling