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Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, asp13asn mutant, an open cap conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 0.15M MALIC ACID, PH 7, 20% PEG3350, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2 38.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.475 α = 90 b = 65.405 β = 90 c = 76.168 γ = 90
Symmetry Space Group P 21 21 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 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 1.5 50 100 0.067 7.4 8 37187 -5 18.419
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 1.5 1.53 100 0.6 3 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 3QU2 1.5 49.63 35951 1152 99.96 0.14545 0.14457 0.17227 0.1814 RANDOM 25.063
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] 0.32 0.42 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_dihedral_angle_4_deg 22.207 r_dihedral_angle_3_deg 14.948 r_scangle_it 9.836 r_scbond_it 7.27 r_dihedral_angle_1_deg 5.717 r_mcangle_it 5.525 r_mcbond_it 3.908 r_rigid_bond_restr 2.546 r_angle_refined_deg 1.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_dihedral_angle_4_deg 22.207 r_dihedral_angle_3_deg 14.948 r_scangle_it 9.836 r_scbond_it 7.27 r_dihedral_angle_1_deg 5.717 r_mcangle_it 5.525 r_mcbond_it 3.908 r_rigid_bond_restr 2.546 r_angle_refined_deg 1.387 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 12
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling