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1.7 Angstrom crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei bound with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 289 100 MM NA/K PHOSPHATE, 50% PEG 200, PH 6.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 3.74 67.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.212 α = 90 b = 100.212 β = 90 c = 110.667 γ = 120
Symmetry Space Group P 63 2 2
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 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 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 1.75 50 98.2 0.098 14.2 14 33131
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 1.75 1.81 100 0.632 14.4
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 3EIY 1.75 50 33036 1689 0.175 0.175 0.2081 0.185 0.2077 RANDOM 14.99
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] 0.55 0.27 0.55 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.198 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 12.379 r_dihedral_angle_1_deg 5.222 r_scangle_it 2.595 r_scbond_it 1.556 r_angle_refined_deg 1.146 r_mcangle_it 0.872 r_angle_other_deg 0.804 r_mcbond_it 0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.198 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 12.379 r_dihedral_angle_1_deg 5.222 r_scangle_it 2.595 r_scbond_it 1.556 r_angle_refined_deg 1.146 r_mcangle_it 0.872 r_angle_other_deg 0.804 r_mcbond_it 0.446 r_mcbond_other 0.105 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1325 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 34
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling