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Crystal structure of MV in complex with LLP and FRU from Mycobacterium vanbaalenii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2 M lithium sulfate,0.1M Tris, pH 8.5,1.26M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.707 α = 90 b = 112.243 β = 112.31 c = 92.098 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 PIXEL DECTRIS PILATUS3 6M 2022-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 1.0 SSRF BL18U1
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 1.92 50 93.2 0.115 0.126 0.05 0.991 11.1 6.3 106452
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 1.92 1.99 90.6 0.545 0.595 0.232 0.767 6.2
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 1.93 45.14 101032 5344 92.7 0.153 0.151 0.1621 0.188 0.1954 RANDOM 16.54
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.78 r_dihedral_angle_4_deg 20.387 r_dihedral_angle_3_deg 13.782 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 5.669 r_long_range_B_other 5.325 r_scangle_other 3.563 r_scbond_it 2.335 r_scbond_other 2.334 r_mcangle_it 1.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.78 r_dihedral_angle_4_deg 20.387 r_dihedral_angle_3_deg 13.782 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 5.669 r_long_range_B_other 5.325 r_scangle_other 3.563 r_scbond_it 2.335 r_scbond_other 2.334 r_mcangle_it 1.969 r_mcangle_other 1.969 r_angle_refined_deg 1.678 r_angle_other_deg 1.395 r_mcbond_it 1.366 r_mcbond_other 1.365 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 9914 Nucleic Acid Atoms Solvent Atoms 1534 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling PHASER phasing HKL-2000 data reduction