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Crystal structure of RovA from Yersinia in complex with a rovA 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 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 = 88.779 α = 90 b = 88.779 β = 90 c = 67.729 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 2.1 37 97.6 0.01 15.3 5.3 39678 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 2.1 2.2 89 0.05 2 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 2.05 76.9 35093 1905 98.56 0.20562 0.20303 0.2593 0.25132 0.2988 RANDOM 65.609
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] 5.54 5.54 -11.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.665 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 20.948 r_dihedral_angle_1_deg 5.649 r_angle_refined_deg 1.664 r_scangle_it 1.662 r_scbond_it 1.272 r_mcangle_it 1.181 r_mcbond_it 0.717 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.665 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 20.948 r_dihedral_angle_1_deg 5.649 r_angle_refined_deg 1.664 r_scangle_it 1.662 r_scbond_it 1.272 r_mcangle_it 1.181 r_mcbond_it 0.717 r_nbtor_refined 0.301 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.229 r_xyhbond_nbd_refined 0.21 r_symmetry_hbond_refined 0.177 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 76 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing