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Crystal Structure of YvdT from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.1M Bis-Tris pH5.5, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.13 70.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.608 α = 90 b = 115.608 β = 90 c = 97.032 γ = 120
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 MARRESEARCH 2004-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.98017 BSRF 3W1A
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 2.3 20 99.8 0.0809 22.04 6.99 31437 31374
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 2.3 2.38 100 0.271 6.98 3128
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 2.3 20 32740 31321 1553 99.2 0.241 0.238 0.234 0.2311 0.255 0.2527 RANDOM 35.3
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] -1.32 3.24 -1.32 2.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.9 c_scangle_it 3.39 c_mcangle_it 2.25 c_scbond_it 2.25 c_mcbond_it 1.38 c_angle_deg 1.3 c_improper_angle_d 0.73 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.9 c_scangle_it 3.39 c_mcangle_it 2.25 c_scbond_it 2.25 c_mcbond_it 1.38 c_angle_deg 1.3 c_improper_angle_d 0.73 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3185 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 28
Software Software Software Name Purpose CNS refinement MAR345 data collection SCALEPACK data scaling SHELXS phasing