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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, glu47asn 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 = 84.72 α = 90 b = 84.72 β = 90 c = 79.213 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 50 97.2 0.076 4.3 6.4 27575 -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 1.87 1.94 95.3 0.76 1.2 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 2 20 21265 703 97.32 0.21816 0.21614 0.2104 0.28339 0.2683 RANDOM 57.068
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] 3.03 1.52 3.03 -4.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.792 r_dihedral_angle_4_deg 17.139 r_dihedral_angle_3_deg 16.667 r_scangle_it 9.589 r_scbond_it 7.582 r_dihedral_angle_1_deg 5.569 r_mcangle_it 5.412 r_mcbond_it 3.845 r_angle_refined_deg 1.256 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.792 r_dihedral_angle_4_deg 17.139 r_dihedral_angle_3_deg 16.667 r_scangle_it 9.589 r_scbond_it 7.582 r_dihedral_angle_1_deg 5.569 r_mcangle_it 5.412 r_mcbond_it 3.845 r_angle_refined_deg 1.256 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.182 r_nbd_refined 0.164 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.088 r_bond_refined_d 0.01 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 1759 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 15
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling