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Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 10mM CaCl2, 0.1M MES, 30% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.8
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.983 α = 71.96 b = 48.765 β = 70.65 c = 57.233 γ = 80.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH 2003-08-14 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.9791 APS 5ID-B
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 1.95 30 0.045 16.318 4 35124 33929 -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 1.95 1.97 88.4 0.279 2.6 2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.95 30 31133 31133 1653 96.99 0.21047 0.20808 0.2513 0.25417 RANDOM 24.601
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] 1.11 1.85 -0.3 -1.94 0.34 0.19
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.749 r_scbond_it 6.323 r_mcangle_it 4.442 r_dihedral_angle_1_deg 4.427 r_mcbond_it 3.378 r_angle_refined_deg 0.947 r_angle_other_deg 0.917 r_symmetry_vdw_other 0.354 r_symmetry_hbond_refined 0.301 r_nbd_other 0.244
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.749 r_scbond_it 6.323 r_mcangle_it 4.442 r_dihedral_angle_1_deg 4.427 r_mcbond_it 3.378 r_angle_refined_deg 0.947 r_angle_other_deg 0.917 r_symmetry_vdw_other 0.354 r_symmetry_hbond_refined 0.301 r_nbd_other 0.244 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.215 r_nbtor_other 0.09 r_chiral_restr 0.055 r_bond_refined_d 0.01 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 3296 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing