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Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.05M Tris-HCl, 0.1M CaCl2, 4% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.011 α = 108.98 b = 80.095 β = 102.25 c = 87.056 γ = 96.14
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 210 mirror 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97909 Photon Factory AR-NW12A
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 2.5 100 98.2 0.091 12.5 7.8 32512 32512 -3 46.7
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 2.5 2.59 98 0.48 7.3 3252
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 2.5 10 31983 30388 1595 98.23 0.22213 0.22023 0.2352 0.25854 0.2332 RANDOM 53.419
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] 0.53 -0.32 -3.16 -1.41 -0.8 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.883 r_dihedral_angle_3_deg 23.504 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_1_deg 6.498 r_scangle_it 3.626 r_scbond_it 2.422 r_angle_refined_deg 2.165 r_mcangle_it 1.809 r_mcbond_it 1.097 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.883 r_dihedral_angle_3_deg 23.504 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_1_deg 6.498 r_scangle_it 3.626 r_scbond_it 2.422 r_angle_refined_deg 2.165 r_mcangle_it 1.809 r_mcbond_it 1.097 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.29 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.244 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.133 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5530 Nucleic Acid Atoms 1136 Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing