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Structure of F420 binding protein Rv1558 from Mycobacterium tuberculosis with F420 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.1 M Sodium citrate pH 5.8, 0.5 M Ammonium sulfate, 1 M Lithium sulfate, and 3 % Glycerol (v/v)
Crystal Properties Matthews coefficient Solvent content 6.47 80.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.544 α = 90 b = 169.544 β = 90 c = 169.544 γ = 90
Symmetry Space Group P 43 3 2
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 EIGER X 16M 2019-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953719973564 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.469 48.99 99.7 0.187 0.028 1 28.5 78.5 30473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.469 2.558 97.54 5.963 0.945 0.416 1.1
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 3R5R 2.469 48.99 28938 1595 99.8 0.20106 0.20003 0.2082 0.22012 0.2261 RANDOM 83.23
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.573 r_dihedral_angle_3_deg 14.91 r_dihedral_angle_4_deg 14.244 r_long_range_B_other 7.481 r_long_range_B_refined 7.466 r_dihedral_angle_1_deg 5.49 r_scangle_other 4.637 r_mcangle_it 3.276 r_mcangle_other 3.275 r_scbond_it 3.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.573 r_dihedral_angle_3_deg 14.91 r_dihedral_angle_4_deg 14.244 r_long_range_B_other 7.481 r_long_range_B_refined 7.466 r_dihedral_angle_1_deg 5.49 r_scangle_other 4.637 r_mcangle_it 3.276 r_mcangle_other 3.275 r_scbond_it 3.225 r_scbond_other 2.991 r_mcbond_it 2.095 r_mcbond_other 2.095 r_angle_refined_deg 1.248 r_angle_other_deg 0.996 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2216 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing