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Structure of MS3494 from Mycobacterium smegmatis bound to sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7REF 7REF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 26 % PEG 4K, 0.2 M Lithium acetate (pH 7.5)
Soaked in 20 % Sucrose
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.463 α = 90 b = 98.463 β = 90 c = 45.581 γ = 120
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 2022-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 1.9 33.469 99.9 0.09 0.095 0.999 20.4 10.2 20058
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 1.9 1.95 0.746 0.784 0.95 4.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7REF 1.901 33.469 20057 958 99.856 0.142 0.1404 0.1467 0.175 0.1803 23.013
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] -1.309 -0.654 -1.309 4.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.418 r_dihedral_angle_3_deg 14.335 r_dihedral_angle_2_deg 10.643 r_lrange_it 6.385 r_lrange_other 6.337 r_dihedral_angle_1_deg 5.823 r_scangle_it 4.943 r_scangle_other 4.941 r_scbond_it 3.237 r_scbond_other 3.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.418 r_dihedral_angle_3_deg 14.335 r_dihedral_angle_2_deg 10.643 r_lrange_it 6.385 r_lrange_other 6.337 r_dihedral_angle_1_deg 5.823 r_scangle_it 4.943 r_scangle_other 4.941 r_scbond_it 3.237 r_scbond_other 3.237 r_mcangle_it 2.829 r_mcangle_other 2.828 r_mcbond_it 1.927 r_mcbond_other 1.913 r_angle_refined_deg 1.472 r_angle_other_deg 0.546 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.211 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.186 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.158 r_ncsr_local_group_1 0.106 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2038 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing