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Crystal structure of putative transcriptional regulator RHA1_ro06953 (IclR-family) from Rhodococcus sp.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG3350 25%, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.247 α = 74.88 b = 69.027 β = 71.47 c = 79.214 γ = 68.87
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 SBC-3 mirrors 2006-06-11 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97904 APS 19-BM
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 2 50 97.3 0.053 0.042 36 4 75273 73258 -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 2 2.07 91.1 0.244 0.228 6.6 3.7 6874
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 (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 36.25 69510 69510 3697 100 0.18482 0.18224 0.182 0.23384 0.2336 RANDOM 30.931
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 0.44 0.11 -1.01 -0.07 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.744 r_dihedral_angle_4_deg 19.321 r_dihedral_angle_3_deg 14.08 r_dihedral_angle_1_deg 6.133 r_scangle_it 4.04 r_scbond_it 2.926 r_angle_refined_deg 1.617 r_mcangle_it 1.541 r_mcbond_it 1.335 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.744 r_dihedral_angle_4_deg 19.321 r_dihedral_angle_3_deg 14.08 r_dihedral_angle_1_deg 6.133 r_scangle_it 4.04 r_scbond_it 2.926 r_angle_refined_deg 1.617 r_mcangle_it 1.541 r_mcbond_it 1.335 r_nbtor_refined 0.307 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 7357 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 phasing RESOLVE model building REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing SHELXE model building DM phasing MLPHARE phasing RESOLVE phasing ARP/wARP model building O model building Coot model building CCP4 phasing