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Crystal structure of YisK from Bacillus subtilis in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other Phyre homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2 M Mg-acetate and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.937 α = 90 b = 93.768 β = 90 c = 125.484 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 PIXEL DECTRIS PILATUS3 6M 2019-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.26 46.93 100 0.117 0.07 0.998 11.9 6.3 30609
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.32 2.209 1.423 0.298
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.26 46.93 28549 1995 99.92 0.21376 0.21094 0.25478 0.2542 RANDOM 64.315
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] -0.99 1.34 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.401 r_dihedral_angle_1_deg 8.109 r_long_range_B_refined 5.273 r_long_range_B_other 5.271 r_scangle_other 3.398 r_mcangle_it 2.889 r_mcangle_other 2.888 r_scbond_other 2.09 r_scbond_it 2.089 r_mcbond_it 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.401 r_dihedral_angle_1_deg 8.109 r_long_range_B_refined 5.273 r_long_range_B_other 5.271 r_scangle_other 3.398 r_mcangle_it 2.889 r_mcangle_other 2.888 r_scbond_other 2.09 r_scbond_it 2.089 r_mcbond_it 1.77 r_mcbond_other 1.77 r_angle_refined_deg 1.141 r_angle_other_deg 0.385 r_chiral_restr 0.055 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4502 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing