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The structure and function of B. subtilis YkoF gene product: ligand free protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 20% PEG 8000, 0.2 M calcium acetate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.76 55.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.93 α = 90 b = 83.28 β = 90 c = 85.9 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARRESEARCH mirrors 2003-08-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9642, 0.9795, 0.9794 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 34 0.24 24 4.1 212643 51209 1 -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) 1.6 1.66 43.4 0.322 1.9 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 1.65 34.3 47795 1265 100 0.17353 0.17223 0.186 0.22375 0.235 RANDOM 23.29
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] 2.9 -0.89 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.344 r_sphericity_free 4.894 r_scangle_it 4.166 r_scbond_it 2.911 r_sphericity_bonded 2.748 r_mcangle_it 2.105 r_rigid_bond_restr 1.691 r_angle_refined_deg 1.517 r_mcbond_it 1.337 r_angle_other_deg 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.344 r_sphericity_free 4.894 r_scangle_it 4.166 r_scbond_it 2.911 r_sphericity_bonded 2.748 r_mcangle_it 2.105 r_rigid_bond_restr 1.691 r_angle_refined_deg 1.517 r_mcbond_it 1.337 r_angle_other_deg 0.885 r_symmetry_vdw_other 0.316 r_symmetry_hbond_refined 0.282 r_nbd_other 0.266 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.209 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.098 r_nbtor_other 0.088 r_metal_ion_refined 0.068 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2819 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHELXS phasing