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Ohr from Xylella fastidiosa in oxidized state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZB8 PDB entry 1ZB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 sodium citrate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.18 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.813 α = 90 b = 83.693 β = 93.67 c = 60.766 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 275 CCD MAR CCD 165 mm 2010-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.43 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 60.63 99.9 13.9 3.1 23908 23868
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 99.9 3 3
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 1ZB8 2.15 60.63 22647 1221 99.73 0.17912 0.17644 0.1892 0.22642 0.2199 RANDOM 21.684
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] 0.16 -0.26 -0.31 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.515 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_3_deg 16.56 r_dihedral_angle_1_deg 8.539 r_scangle_it 2.425 r_angle_refined_deg 1.538 r_scbond_it 1.472 r_mcangle_it 1.015 r_mcbond_it 0.576 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.515 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_3_deg 16.56 r_dihedral_angle_1_deg 8.539 r_scangle_it 2.425 r_angle_refined_deg 1.538 r_scbond_it 1.472 r_mcangle_it 1.015 r_mcbond_it 0.576 r_nbtor_refined 0.305 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3060 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement