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Crystal structure of transcriptional regulator, GntR family from Bacillus cereus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 297 0.2M MgCl2, 0.1M Tris-Cl pH 8.5, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 5.88 79.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.191 α = 90 b = 121.191 β = 90 c = 114.693 γ = 90
Symmetry Space Group P 41 21 2
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 315r 2009-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 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 2.9 50 100 0.139 29.67 14.2 19581 19580 -3
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 2.9 2.95 100 0.771 4.17 14.5 968
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 2.9 50 19505 19505 994 99.82 0.20554 0.20554 0.20355 0.2111 0.24324 0.2471 RANDOM 31.483
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] -3.52 -3.52 7.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.139 r_dihedral_angle_3_deg 16.144 r_dihedral_angle_4_deg 11.138 r_dihedral_angle_1_deg 6.476 r_scangle_it 2.751 r_scbond_it 1.548 r_angle_refined_deg 1.304 r_mcangle_it 0.98 r_mcbond_it 0.496 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.139 r_dihedral_angle_3_deg 16.144 r_dihedral_angle_4_deg 11.138 r_dihedral_angle_1_deg 6.476 r_scangle_it 2.751 r_scbond_it 1.548 r_angle_refined_deg 1.304 r_mcangle_it 0.98 r_mcbond_it 0.496 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 16
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing