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FGD2 (Rv0132c) from Mycobacterium tuberculosis with cofactor F420 crystallised with Anderson-Evans polyoxotungstate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 0.12M Monosaccharides, 0.1M buffer system 1 pH 6.5 (MES imidazole), 37.5% precipitant mix 4 Morpheus condition F4
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.31 α = 90 b = 89.311 β = 90 c = 155.634 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 99 PIXEL DECTRIS EIGER2 XE 16M 2021-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.35 77.82 100 0.282 0.293 0.08 0.996 6.2 13.1 51484
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 2.35 2.42 100 1.04 1.088 0.317 0.895 2.1 11.5
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 THROUGHOUT 2.35 77.82 51398 2612 99.959 0.213 0.2105 0.2113 0.2508 0.2515 21.907
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] -0.776 -1.287 2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.606 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_2_deg 8.049 r_dihedral_angle_1_deg 6.734 r_lrange_it 4.895 r_scangle_it 2.496 r_angle_refined_deg 1.889 r_scbond_it 1.758 r_mcangle_it 1.138 r_metal_ion_refined 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.606 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_2_deg 8.049 r_dihedral_angle_1_deg 6.734 r_lrange_it 4.895 r_scangle_it 2.496 r_angle_refined_deg 1.889 r_scbond_it 1.758 r_mcangle_it 1.138 r_metal_ion_refined 0.763 r_mcbond_it 0.67 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.303 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.122 r_ncsr_local_group_4 0.081 r_ncsr_local_group_1 0.077 r_ncsr_local_group_6 0.077 r_ncsr_local_group_3 0.068 r_ncsr_local_group_5 0.053 r_ncsr_local_group_2 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9784 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 345
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing