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Structural Genomics, the crystal structure of the C-terminal domain of Yurk from Bacillus subtilis subsp. subtilis str. 168
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.7 293 1.9M Ammonium sulfate,
0.1M Tris, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.509 α = 90 b = 104.704 β = 118.58 c = 40.538 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315 mirror 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 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 1.8 35.6 99.1 0.099 37.9 8.5 27240 27240
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) 1.8 1.86 95.3 0.461 3.57 5.3 2631
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 1.8 35.6 25821 25821 1364 98.78 0.19612 0.19612 0.19429 0.1955 0.23029 0.1985 RANDOM 31.412
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] 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.029 r_dihedral_angle_3_deg 17.888 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_1_deg 7.048 r_scangle_it 5.472 r_scbond_it 4.011 r_mcangle_it 2.325 r_angle_refined_deg 2.201 r_mcbond_it 1.492 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.029 r_dihedral_angle_3_deg 17.888 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_1_deg 7.048 r_scangle_it 5.472 r_scbond_it 4.011 r_mcangle_it 2.325 r_angle_refined_deg 2.201 r_mcbond_it 1.492 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.224 r_chiral_restr 0.161 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.145 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 2359 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building