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Crystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 289 1M Sodium-potassium phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.277 α = 90 b = 114.277 β = 90 c = 175.359 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 mirror 2007-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97925 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 2.05 36.6 99.4 0.096 16.7 3.1 159207 159207 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 2.05 2.11 98.4 0.587 1.7 2.9 13206
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.05 36.6 151134 151134 7989 99.35 0.17823 0.17823 0.17504 0.1773 0.23853 0.2389 RANDOM 33.308
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 21.673 r_dihedral_angle_3_deg 20.767 r_dihedral_angle_1_deg 7.317 r_scangle_it 4.519 r_scbond_it 3.007 r_angle_refined_deg 1.985 r_mcangle_it 1.65 r_mcbond_it 1.269 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 21.673 r_dihedral_angle_3_deg 20.767 r_dihedral_angle_1_deg 7.317 r_scangle_it 4.519 r_scbond_it 3.007 r_angle_refined_deg 1.985 r_mcangle_it 1.65 r_mcbond_it 1.269 r_nbtor_refined 0.315 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.162 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 18888 Nucleic Acid Atoms Solvent Atoms 1349 Heterogen Atoms 380
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing HKL-3000 phasing