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2.2 A crystal structure of inorganic pyrophosphatase from rickettsia prowazekii (p21 form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 10.5 293 30% PEG 400, 100 mM CAPS, pH 10.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.96 α = 90 b = 107.35 β = 96.05 c = 128.42 γ = 90
Symmetry Space Group P 1 21 1
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 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 2.2 128.037 93.6 0.07 0.07 8.689 3.2 330779 103788
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) 2.2 2.32 88.5 0.51 0.51 1.4 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 30 98484 5260 93.66 0.22934 0.22733 0.2338 0.26659 0.2506 RANDOM 40.172
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] 1.01 -0.35 -1.34 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.354 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 20.527 r_dihedral_angle_1_deg 7.295 r_scangle_it 3.451 r_scbond_it 2.174 r_angle_refined_deg 1.826 r_mcangle_it 1.517 r_angle_other_deg 1.222 r_mcbond_it 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.354 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 20.527 r_dihedral_angle_1_deg 7.295 r_scangle_it 3.451 r_scbond_it 2.174 r_angle_refined_deg 1.826 r_mcangle_it 1.517 r_angle_other_deg 1.222 r_mcbond_it 0.835 r_mcbond_other 0.252 r_chiral_restr 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 15743 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 26
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction