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2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EIP PDB entry 2EIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 2.5M NaCl, 0.1M Na acetate pH 4.5, 0.2M Li2SO4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.97 α = 90 b = 115.23 β = 90 c = 139.73 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 100 CCD ADSC QUANTUM 210 Adjustable focusing mirrors 2008-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1
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 2.2 34.94 98.8 0.132 0.132 5 6.2 56518
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 2.2 2.32 97.6 0.524 0.524 1.5 5.9 8016
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2EIP 2.2 33.56 56507 2855 98.53 0.22 0.217 0.28 0.2381 RANDOM 20.576
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 18.916 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_1_deg 5.901 r_scangle_it 2.302 r_scbond_it 1.44 r_angle_refined_deg 1.277 r_mcangle_it 1.045 r_mcbond_it 0.601 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 18.916 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_1_deg 5.901 r_scangle_it 2.302 r_scbond_it 1.44 r_angle_refined_deg 1.277 r_mcangle_it 1.045 r_mcbond_it 0.601 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8072 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 38
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction