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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, glu47ala mutant complexed with sulfate
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 8.5 294 0.1M TRIS-HCL, PH 8.5, 30% PEG4000, 200MM LITHIUM SULFATE, 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 = 85.382 α = 90 b = 85.382 β = 90 c = 78.915 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 1.9 40 99.1 0.137 4.6 4.4 27369 -5 37.003
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 1.97 99.6 0.77 1 3.4
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 25682 846 99.85 0.19918 0.19782 0.199 0.24274 0.2418 RANDOM 43.083
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] 1.96 0.98 1.96 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.447 r_dihedral_angle_4_deg 25.316 r_dihedral_angle_3_deg 15.603 r_scangle_it 8.219 r_scbond_it 6.425 r_dihedral_angle_1_deg 5.522 r_mcangle_it 4.724 r_mcbond_it 3.42 r_angle_refined_deg 1.253 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.447 r_dihedral_angle_4_deg 25.316 r_dihedral_angle_3_deg 15.603 r_scangle_it 8.219 r_scbond_it 6.425 r_dihedral_angle_1_deg 5.522 r_mcangle_it 4.724 r_mcbond_it 3.42 r_angle_refined_deg 1.253 r_nbtor_refined 0.293 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.175 r_nbd_refined 0.155 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.081 r_bond_refined_d 0.01 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_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 1737 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 5
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling