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Crystal structure of transcriptional regulator, a member of PadR family, from Enterococcus faecalis V583
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.05 M Ammonium Sulfate, 50mM Bis-Tris 6.5, 30% Pentaerythritol Ethoxylate (15/4 EO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.766 α = 90 b = 86.766 β = 90 c = 84.731 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 QUANTUM 315 mirrors 2007-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 2.7 40 99.6 0.064 33 4.7 6530 6515 2 2 62
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 2.7 2.75 100 0.144 12 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SAD THROUGHOUT 2.7 20 2 2 6510 6207 302 99.3 0.23 0.223 0.22088 0.2289 0.26269 0.2692 RANDOM 22.086
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] -3.97 -1.99 -3.97 5.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.665 r_dihedral_angle_4_deg 15.594 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.626 r_angle_refined_deg 0.929 r_scangle_it 0.835 r_angle_other_deg 0.74 r_scbond_it 0.486 r_mcangle_it 0.444 r_mcbond_it 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.665 r_dihedral_angle_4_deg 15.594 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.626 r_angle_refined_deg 0.929 r_scangle_it 0.835 r_angle_other_deg 0.74 r_scbond_it 0.486 r_mcangle_it 0.444 r_mcbond_it 0.237 r_chiral_restr 0.052 r_mcbond_other 0.023 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1689 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 16
Software Software Software Name Purpose SBC-Collect data collection SHELX model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing