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X-ray crystal structure of YusO protein from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 294 Ammonium Sulfate, Bis-Tris, Pentaerythritol Ethoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.19 43.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.029 α = 90 b = 71.912 β = 90 c = 96.642 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 100 CCD SBC-2 2003-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.25 50 99.5 0.101 8 13.59 16195
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) 2.25 2.3 94.5 0.51
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 2.25 33.71 15104 13908 1196 97.8 0.221 0.219 0.2224 0.273 0.2319 RANDOM 34.54
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] 0.84 0.34 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.02 r_scangle_it 4.189 r_scbond_it 2.385 r_mcangle_it 1.498 r_angle_refined_deg 1.222 r_mcbond_it 0.771 r_angle_other_deg 0.747 r_symmetry_vdw_other 0.308 r_nbd_other 0.231 r_nbd_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.02 r_scangle_it 4.189 r_scbond_it 2.385 r_mcangle_it 1.498 r_angle_refined_deg 1.222 r_mcbond_it 0.771 r_angle_other_deg 0.747 r_symmetry_vdw_other 0.308 r_nbd_other 0.231 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.192 r_symmetry_vdw_refined 0.135 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.083 r_chiral_restr 0.067 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 2231 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXD phasing autoSHARP phasing