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Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 293 0.2M Ca Chloride, 0.1M HEPES pH 7.4, 20% PEG3350, 0.3M NDSB195, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.721 α = 102.31 b = 52.23 β = 107.25 c = 72.853 γ = 89.71
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 mirror 2006-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97907 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 1.8 50 96.7 0.07 0.063 24.6 2.3 63744 61651 -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 1.8 1.83 94.6 0.402 0.376 1.9 2.3 3019
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 1.8 25.8 58508 58508 3130 95.47 0.17881 0.17664 0.1982 0.21946 0.2333 RANDOM 33.106
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] 0.4 -0.21 0.15 -0.26 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.36 r_dihedral_angle_4_deg 17.997 r_dihedral_angle_3_deg 14.953 r_dihedral_angle_1_deg 5.341 r_scangle_it 4.769 r_scbond_it 3.295 r_mcangle_it 1.563 r_angle_refined_deg 1.508 r_mcbond_it 1.097 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.36 r_dihedral_angle_4_deg 17.997 r_dihedral_angle_3_deg 14.953 r_dihedral_angle_1_deg 5.341 r_scangle_it 4.769 r_scbond_it 3.295 r_mcangle_it 1.563 r_angle_refined_deg 1.508 r_mcbond_it 1.097 r_nbtor_refined 0.303 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.214 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.107 r_bond_refined_d 0.019 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5289 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing Coot model building CCP4 phasing O model building ARP/wARP model building