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Crystal structure of B. subtilis YdzF in reduced 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 298 Protein buffer: 50 mM HEPES-Na, pH 7.5, 100 mM NaCl, 5% (v/v) glycerol, and 0.1 mM TCEP. Crystallization solution: 100 mM Sodium acetate trihydrate, pH 4.6, 2.0 M Sodium formate. Protein and crystallization solution were mixed in a 1:1 ratio (microbatch under 1:1 paraffin oil to silicon oil).
Crystal Properties Matthews coefficient Solvent content 2.57 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.07 α = 90 b = 119.03 β = 90 c = 79.92 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 2023-11-10 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 2.54 41.95 98.6 0.082 0.1 0.055 0.989 7.3 3.04 18602 36.15
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 2.54 2.65 97.8 0.404 0.488 0.269 0.575 2.5 3.07
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 2.54 41.95 18602 1025 98.195 0.246 0.2426 0.2452 0.3084 0.3117 47.365
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] 2.235 0.856 -3.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.666 r_dihedral_angle_6_deg 17.611 r_lrange_it 17.549 r_lrange_other 17.523 r_dihedral_angle_3_deg 15.59 r_scangle_it 13.748 r_scangle_other 13.745 r_mcangle_it 13.086 r_mcangle_other 13.085 r_scbond_it 9.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.666 r_dihedral_angle_6_deg 17.611 r_lrange_it 17.549 r_lrange_other 17.523 r_dihedral_angle_3_deg 15.59 r_scangle_it 13.748 r_scangle_other 13.745 r_mcangle_it 13.086 r_mcangle_other 13.085 r_scbond_it 9.432 r_scbond_other 9.431 r_mcbond_it 8.166 r_mcbond_other 8.156 r_rigid_bond_restr 6.431 r_dihedral_angle_1_deg 5.907 r_angle_refined_deg 1.952 r_angle_other_deg 0.624 r_symmetry_nbd_refined 0.311 r_nbd_other 0.268 r_nbd_refined 0.243 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.182 r_xyhbond_nbd_refined 0.139 r_ncsr_local_group_3 0.114 r_ncsr_local_group_1 0.11 r_ncsr_local_group_4 0.104 r_ncsr_local_group_6 0.098 r_ncsr_local_group_2 0.094 r_ncsr_local_group_5 0.091 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2757 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms
Software Software Software Name Purpose Coot model building REFMAC refinement PHASER phasing Aimless data scaling iMOSFLM data reduction MAR345dtb data collection