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Structure of the family II inorganic pyrophosphatase from Streptococcus agalactiae at 2.8 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I74 PDB ENTRY 1I74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 298 0.4M ammonium phosphate monobasic, pH 4.2, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.96 α = 90 b = 181.96 β = 90 c = 132.61 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 19.5 99.6 0.14 0.14 12.3 4.2 20708 20700 -3 -3 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 96.2 0.3 0.3 6.2 4.4 1903
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 1I74 2.8 19.5 19668 1036 100 0.19565 0.1919 0.1919 0.26695 0.2664 RANDOM 18.164
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] -1.2 -0.6 -1.2 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.281 r_dihedral_angle_3_deg 19.307 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.513 r_nbtor_refined 0.309 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.281 r_dihedral_angle_3_deg 19.307 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.513 r_nbtor_refined 0.309 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.094 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4714 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection XDS data reduction XSCALE data scaling MOLREP phasing