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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, asp13ala mutant
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 6 291 0.1M MES, PH 6.0, 20% PEG8000, 200MM CALCIUM ACETATE, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.945 α = 89.97 b = 76.217 β = 89.97 c = 95.588 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2009-09-30 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 93.2 0.101 4.5 1.7 133986 -5 30.3
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 2.07 83.9 0.73 0.6 1.7
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 2.1 20 104324 3211 93.41 0.21846 0.21639 0.2192 0.28583 0.2853 RANDOM 36.214
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] -2.27 0.26 -0.04 -1.08 0.22 3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.073 r_dihedral_angle_3_deg 16.318 r_dihedral_angle_4_deg 11.7 r_scangle_it 9.556 r_scbond_it 7.401 r_dihedral_angle_1_deg 5.319 r_mcangle_it 4.573 r_mcbond_it 3.229 r_angle_refined_deg 1.177 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.073 r_dihedral_angle_3_deg 16.318 r_dihedral_angle_4_deg 11.7 r_scangle_it 9.556 r_scbond_it 7.401 r_dihedral_angle_1_deg 5.319 r_mcangle_it 4.573 r_mcbond_it 3.229 r_angle_refined_deg 1.177 r_chiral_restr 0.078 r_bond_refined_d 0.009 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 13976 Nucleic Acid Atoms Solvent Atoms 982 Heterogen Atoms 28
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling