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The DNA-binding domain of L-lactate utilization repressor (LutR-DBD) from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ITasser
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Morpheus screen solution:
0.1 M sodium HEPES/MOPS (acid) buffer system (pH 7.5), 37.5% (v/v) 2 methyl 2,4 pentanediol, 37.5% (v/v) PEG 1000, 37.5% (v/v) PEG 3350, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI
Volume ratio (protein:solution) = 1ul : 2ul
Plate: EasyXtal 15 well plate (NeXtal Biotechnologies, Holland)
Crystal Properties Matthews coefficient Solvent content 1.79 30.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.31 α = 90 b = 38.37 β = 90 c = 66.71 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 PIXEL DECTRIS PILATUS 6M 2022-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9797 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.46 50 100 0.067 0.073 0.9990000000000001 12.26 6.76 24387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.55 3.1189999999999998 3.388 0.319
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.46 33.38 12527 660 99.98 0.20402 0.20221 0.2086 0.23735 0.239 RANDOM 40.221
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] 0.77 -0.95 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.925 r_dihedral_angle_2_deg 13.993 r_long_range_B_refined 13.299 r_long_range_B_other 13.038 r_scangle_other 7.679 r_mcangle_it 7.112 r_mcangle_other 7.111 r_dihedral_angle_1_deg 6.272 r_scbond_other 5.15 r_scbond_it 5.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.925 r_dihedral_angle_2_deg 13.993 r_long_range_B_refined 13.299 r_long_range_B_other 13.038 r_scangle_other 7.679 r_mcangle_it 7.112 r_mcangle_other 7.111 r_dihedral_angle_1_deg 6.272 r_scbond_other 5.15 r_scbond_it 5.147 r_mcbond_it 4.382 r_mcbond_other 4.37 r_angle_refined_deg 1.572 r_angle_other_deg 0.556 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 593 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing