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Crystal structure of an essential response regulator DNA binding domain, VicRc in Enterococcus faecalis, a member of the YycF subfamily.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPC PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ experimental model PDB 1YS6 PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ experimental model PDB 1P2F PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ experimental model PDB 1GXQ PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 1.8M ammonium sulphate, 0.1M sodium citrate, 3% dimethyl sulfoxide, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.71 28.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.235 α = 90 b = 36.235 β = 90 c = 73.935 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal Max-Flux 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 36.226 99.5 0.053 0.053 11.2 6.2 7524 7524 27.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98.9 0.347 0.347 4.8 5.7 1083
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 (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 ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ 1.9 12 7545 7134 345 99.57 0.18114 0.17865 0.1806 0.23619 0.2386 RANDOM 19.596
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] 0.77 0.77 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.973 r_dihedral_angle_4_deg 19.526 r_dihedral_angle_3_deg 18.347 r_dihedral_angle_1_deg 6.899 r_scangle_it 3.674 r_scbond_it 2.36 r_angle_refined_deg 1.497 r_mcangle_it 1.407 r_mcbond_it 0.864 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.973 r_dihedral_angle_4_deg 19.526 r_dihedral_angle_3_deg 18.347 r_dihedral_angle_1_deg 6.899 r_scangle_it 3.674 r_scbond_it 2.36 r_angle_refined_deg 1.497 r_mcangle_it 1.407 r_mcbond_it 0.864 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.103 r_bond_refined_d 0.013 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 844 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing