☰ Navigation Tabs
Crystal structure of B. subtilis YdzF in oxidized state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-O31494-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 298 Protein buffer: 50 mM HEPES-Na, pH 7.5, 100 mM NaCl, 5% (v/v) glycerol. Crystallization solution: 200 mM sodium citrate tribasic dihydrate, 100 mM HEPES-Na, pH 7.5, 30% (v/v) (+/-)-2-methyl-2,4-pentanediol (MPD). Protein and crystallization solution were mixed 1:1 (microbatch under 1:1 paraffin oil to silicon oil).
Crystal Properties Matthews coefficient Solvent content 2.77 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.43 α = 90 b = 118.5 β = 90 c = 80.24 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MAR scanner 345 mm plate 2023-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 57.83 98.7 0.079 0.098 0.056 0.995 5.7 2.83 25498 37.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.35 97 0.405 0.501 0.292 0.309 2.5 2.75
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.262 41.706 25490 1234 96.134 0.226 0.2238 0.2337 0.276 0.2913 47.612
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] 18.307 7.861 -26.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.397 r_lrange_it 22.887 r_lrange_other 22.887 r_dihedral_angle_3_deg 19.715 r_dihedral_angle_6_deg 16.099 r_scangle_it 14.774 r_scangle_other 14.771 r_mcangle_it 13.111 r_mcangle_other 13.108 r_scbond_it 10.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.397 r_lrange_it 22.887 r_lrange_other 22.887 r_dihedral_angle_3_deg 19.715 r_dihedral_angle_6_deg 16.099 r_scangle_it 14.774 r_scangle_other 14.771 r_mcangle_it 13.111 r_mcangle_other 13.108 r_scbond_it 10.188 r_scbond_other 10.185 r_mcbond_it 8.42 r_mcbond_other 8.417 r_rigid_bond_restr 7.076 r_dihedral_angle_1_deg 4.271 r_angle_refined_deg 1.637 r_angle_other_deg 0.569 r_symmetry_xyhbond_nbd_refined 0.38 r_nbd_other 0.315 r_symmetry_nbd_refined 0.302 r_nbd_refined 0.245 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.196 r_ncsr_local_group_6 0.183 r_ncsr_local_group_3 0.178 r_ncsr_local_group_5 0.174 r_ncsr_local_group_1 0.167 r_ncsr_local_group_2 0.165 r_ncsr_local_group_4 0.159 r_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2927 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 12
Software Software Software Name Purpose Coot model building REFMAC refinement PHASER phasing PARROT phasing Aimless data scaling iMOSFLM data reduction MAR345dtb data collection