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Crystal structure of YckF from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG 8000, Na cacodylate, Ca acetate, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.08 α = 90 b = 72.08 β = 90 c = 245.56 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD CUSTOM-MADE Sagitally focusing double crystal monochromator and vertically focusing mirror 2002-03-17 M MAD 2 1 x-ray 110 CCD CUSTOM-MADE Sagitally focusing double crystal monochromator and vertically focusing mirror 2002-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9795, 0.9793, 0.9537 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-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 1,2 1.95 60 99.6 0.072 31.6 28687 28572
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.01 100 0.468 5 2457
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.95 62.02 28572 26023 1389 95.85 0.18897 0.18897 0.18708 0.22493 RANDOM 18.524
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] 0.45 0.23 0.45 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.146 r_dihedral_angle_1_deg 5.646 r_scangle_it 4.486 r_scbond_it 2.941 r_mcangle_it 1.875 r_angle_refined_deg 1.814 r_angle_other_deg 1.176 r_mcbond_it 1.129 r_symmetry_vdw_other 0.284 r_nbd_other 0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.146 r_dihedral_angle_1_deg 5.646 r_scangle_it 4.486 r_scbond_it 2.941 r_mcangle_it 1.875 r_angle_refined_deg 1.814 r_angle_other_deg 1.176 r_mcbond_it 1.129 r_symmetry_vdw_other 0.284 r_nbd_other 0.268 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.11 r_nbtor_other 0.092 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2807 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement dtDisplay data collection HKL-2000 data reduction CNS refinement d*TREK data scaling d*TREK data reduction DTDISPLAY data reduction HKL-2000 data scaling CNS phasing