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Crystal structure of RovA from Yersinia in complex with an invasin promoter fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DEU PDB ENTRY 3DEU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 10 MM MGCL2, 50 MM MES PH 5.6, 2.3 M LISO4
Crystal Properties Matthews coefficient Solvent content 3.33 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.678 α = 90 b = 88.678 β = 90 c = 67.503 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 CCD 2010-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.85 76 98.2 0.034 13.9 2.6 49796 2
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 1.85 2.1 99.9 0.487 2.5 2.5
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 3DEU 1.85 76.81 47218 2504 97.97 0.19988 0.19833 0.2532 0.23025 0.2839 RANDOM 50.527
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] 6.61 6.61 -13.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.632 r_dihedral_angle_4_deg 19.733 r_dihedral_angle_3_deg 17.523 r_dihedral_angle_1_deg 4.399 r_angle_refined_deg 1.281 r_scangle_it 1.277 r_scbond_it 0.902 r_mcangle_it 0.808 r_mcbond_it 0.477 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.632 r_dihedral_angle_4_deg 19.733 r_dihedral_angle_3_deg 17.523 r_dihedral_angle_1_deg 4.399 r_angle_refined_deg 1.281 r_scangle_it 1.277 r_scbond_it 0.902 r_mcangle_it 0.808 r_mcbond_it 0.477 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2227 Nucleic Acid Atoms 855 Solvent Atoms 184 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing