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Crystal structure of inorganic pyrophosphatase from Bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FQ3 PDB entry 3FQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.79 290 Internal tracking number 223591H12. Focus screen
based on PACT D6. 100 mM MMT Buffer pH 9.79, 27.04 (%w/v) Polyethylene glycol 1500
BaheA00347aA1_PS00395 at 66.9 mg/ml., VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.86 α = 90.37 b = 68.96 β = 113.38 c = 74.48 γ = 119.79
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2011-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033170 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 95.6 0.05 12.91 2.9 68367 -3 36.44
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 2.05 95.2 0.404 2.6 3
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 MR THROUGHOUT PDB entry 3FQ3 2 36.63 68364 3442 95.85 0.187 0.185 0.1908 0.23 0.2338 RANDOM 33.502
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] -0.36 0.2 1.38 -0.42 0.21 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.922 r_dihedral_angle_4_deg 18.01 r_dihedral_angle_3_deg 14.48 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.598 r_scbond_it 2.238 r_angle_refined_deg 1.446 r_mcangle_it 1.429 r_angle_other_deg 0.886 r_mcbond_it 0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.922 r_dihedral_angle_4_deg 18.01 r_dihedral_angle_3_deg 14.48 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.598 r_scbond_it 2.238 r_angle_refined_deg 1.446 r_mcangle_it 1.429 r_angle_other_deg 0.886 r_mcbond_it 0.771 r_mcbond_other 0.186 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7936 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 54
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction