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Crystal structure of inorganic pyrophosphatase from Ehrlichia chaffeensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INO pdb deposition 1INO modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 HR CRYSTAL SCREEN HT C8: 2.0M AMMONIUM SULPHATE, EHCHA.01623.A AT 27MG/ML, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.85 33.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.71 α = 90 b = 69.71 β = 90 c = 172.07 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 CCD ADSC QUANTUM 315r 2010-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 1.95 50 99.5 0.043 37.08 10.5 12091 12025 -3 37.23
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) 1.95 2 99.8 0.536 4.3 9.5 874
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 deposition 1INO modified with CCP4 program CHAINSAW 1.95 34.85 12091 12024 551 99.5 0.213 0.213 0.211 0.261 0.2492 RANDOM 25.51
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] -0.25 -0.13 -0.25 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.134 r_dihedral_angle_4_deg 15.42 r_dihedral_angle_3_deg 12.356 r_dihedral_angle_1_deg 5.886 r_scangle_it 3.88 r_scbond_it 2.449 r_mcangle_it 1.713 r_angle_refined_deg 1.396 r_mcbond_it 0.936 r_angle_other_deg 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.134 r_dihedral_angle_4_deg 15.42 r_dihedral_angle_3_deg 12.356 r_dihedral_angle_1_deg 5.886 r_scangle_it 3.88 r_scbond_it 2.449 r_mcangle_it 1.713 r_angle_refined_deg 1.396 r_mcbond_it 0.936 r_angle_other_deg 0.857 r_mcbond_other 0.206 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 1202 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 5
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling