☰ Navigation Tabs
YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1M sodium cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.37 α = 104.38 b = 50.42 β = 90.61 c = 89.41 γ = 112.05
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 2003-12-04 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.979 APS 5ID-B
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 1.7 30 0.085 0.072 6.4 6.2 75437 70594 -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 1.7 1.744 67.1 0.298 0.21 3.1 3.8
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 1.7 30 74337 70594 3743 93.58 0.18798 0.18644 0.198 0.21708 0.2247 RANDOM 17.271
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] 0.18 0.27 0.09 0.18 0.12 -0.11
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.909 r_scbond_it 4.989 r_dihedral_angle_1_deg 4.589 r_mcangle_it 3.334 r_mcbond_it 2.225 r_angle_refined_deg 0.898 r_angle_other_deg 0.667 r_symmetry_vdw_other 0.256 r_nbd_other 0.239 r_nbd_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.909 r_scbond_it 4.989 r_dihedral_angle_1_deg 4.589 r_mcangle_it 3.334 r_mcbond_it 2.225 r_angle_refined_deg 0.898 r_angle_other_deg 0.667 r_symmetry_vdw_other 0.256 r_nbd_other 0.239 r_nbd_refined 0.211 r_metal_ion_refined 0.184 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.177 r_nbtor_other 0.09 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.001 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_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 5690 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing RESOLVE phasing