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Xanthomonas XopD C470A Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 15 mg/mL protein in 20 mM Tris-HCl pH 7.5, 75 mM KCl, and 0.5 mM DTT and 1.4 - 1.6 M sodium potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.29 46.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.953 α = 90 b = 91.953 β = 90 c = 45.013 γ = 90
Symmetry Space Group P 41 21 2
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 SBC-3 2005-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97905 APS 19-BM
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 1.8 25.33 94.2 0.075 30.6 7.6 17346 17346 30.5
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 1.8 1.84 77.4 0.58 1.95 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2OIV 1.8 25.33 17317 16804 513 100 0.21191 0.21191 0.21047 0.2095 0.25903 0.2664 RANDOM 33.158
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] -1.75 -1.75 3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.339 r_dihedral_angle_4_deg 20.876 r_dihedral_angle_3_deg 14.385 r_dihedral_angle_1_deg 5.576 r_scangle_it 3.468 r_scbond_it 2.377 r_mcangle_it 1.703 r_angle_refined_deg 1.574 r_mcbond_it 1.084 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.339 r_dihedral_angle_4_deg 20.876 r_dihedral_angle_3_deg 14.385 r_dihedral_angle_1_deg 5.576 r_scangle_it 3.468 r_scbond_it 2.377 r_mcangle_it 1.703 r_angle_refined_deg 1.574 r_mcbond_it 1.084 r_nbtor_refined 0.307 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1408 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing