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Structural Genomics, the crystal structure of the N-terminal domain of the putative transcriptional regulator ybbH from Bacillus subtilis subsp. subtilis str. 168.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.1M Sodium acetate, 2M Ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.898 α = 90 b = 48.06 β = 119.92 c = 58.854 γ = 90
Symmetry Space Group P 1 2 1
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 2006-10-07 M SINGLE WAVELENGTH
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) 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 1.75 25.52 98.2 0.069 40.35 6.7 28223 28223 32.87
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) 1.75 1.81 86.7 0.478 2.42 5.4 2481
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 1.75 25.52 26813 26813 1400 97.86 0.18282 0.18282 0.1811 0.1828 0.21452 0.1896 RANDOM 39.535
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.794 r_dihedral_angle_4_deg 16.373 r_dihedral_angle_3_deg 15.373 r_dihedral_angle_1_deg 5.202 r_scangle_it 4.45 r_scbond_it 2.796 r_mcangle_it 2.145 r_angle_refined_deg 1.725 r_mcbond_it 1.309 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.794 r_dihedral_angle_4_deg 16.373 r_dihedral_angle_3_deg 15.373 r_dihedral_angle_1_deg 5.202 r_scangle_it 4.45 r_scbond_it 2.796 r_mcangle_it 2.145 r_angle_refined_deg 1.725 r_mcbond_it 1.309 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.101 r_bond_refined_d 0.018 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 1924 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing