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CspB from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-I6WZM9-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 No.B5 of Nuc-Pro 3 (1.7 M lithium sulfate, 50 mM HEPES sodium salt, pH 7.0, 50 mM magnesium sulfate) (Jena Bioscience, Germany)
Crystal Properties Matthews coefficient Solvent content 4.85 74.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.573 α = 90 b = 91.573 β = 90 c = 59.805 γ = 120
Symmetry Space Group P 31 2 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 RIGAKU HyPix-3000 2025-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.6 80 99.2 0.206 9.95 7.4 3524
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.73 100 0.73 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AF-I6WZM9-F1 3.6 21.18 3360 145 99.12 0.22949 0.22471 0.2326 0.34665 0.3495 RANDOM 100.212
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] 2.08 1.04 2.08 -6.75
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.554 r_long_range_B_other 24.547 r_dihedral_angle_2_deg 21.127 r_scangle_other 17.948 r_dihedral_angle_3_deg 16.068 r_mcangle_it 15.883 r_mcangle_other 15.876 r_scbond_it 10.763 r_scbond_other 10.753 r_mcbond_it 9.989
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.554 r_long_range_B_other 24.547 r_dihedral_angle_2_deg 21.127 r_scangle_other 17.948 r_dihedral_angle_3_deg 16.068 r_mcangle_it 15.883 r_mcangle_other 15.876 r_scbond_it 10.763 r_scbond_other 10.753 r_mcbond_it 9.989 r_mcbond_other 9.962 r_dihedral_angle_1_deg 7.634 r_angle_refined_deg 1.643 r_angle_other_deg 0.584 r_chiral_restr 0.069 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 950 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing