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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with phosphate, a closed cap conformation
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 8.2 294 0.056M SODIUM PHOSPHATE MONOBASIC, PH 8.2, 1.344M POTASSIUM PHOSPHATE DIBASIC, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 3.16 61.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.578 α = 90 b = 84.578 β = 90 c = 79.271 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 2010-01-23 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 2 50 99.7 0.078 7.4 8 22599 -5 41.734
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 2 2.03 98.7 0.9 1 4.7
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 2 20 20726 683 95.02 0.19298 0.19144 0.2353 0.2428 0.2235 RANDOM 58.119
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] 3.65 1.82 3.65 -5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.434 r_dihedral_angle_3_deg 17.169 r_dihedral_angle_4_deg 17.142 r_scangle_it 13.263 r_scbond_it 10.528 r_mcangle_it 7.408 r_mcbond_it 5.612 r_dihedral_angle_1_deg 5.498 r_angle_refined_deg 1.293 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.434 r_dihedral_angle_3_deg 17.169 r_dihedral_angle_4_deg 17.142 r_scangle_it 13.263 r_scbond_it 10.528 r_mcangle_it 7.408 r_mcbond_it 5.612 r_dihedral_angle_1_deg 5.498 r_angle_refined_deg 1.293 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1743 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 11
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling