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F420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ULE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-2
Crystal Properties Matthews coefficient Solvent content 1.95 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.238 α = 90 b = 68.238 β = 90 c = 91.807 γ = 90
Symmetry Space Group P 41 2 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 2018-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.83 48.3 100 0.039 0.998 13.7 13.7 19796
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.88 100 0.333 0.599
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 FREE R-VALUE 1.83 48.298 19775 940 99.843 0.198 0.197 0.2041 0.2191 0.2273 28.422
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] -0.031 -0.031 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.252 r_dihedral_angle_4_deg 15.471 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 6.776 r_lrange_it 3.201 r_lrange_other 3.155 r_scangle_other 1.926 r_scangle_it 1.917 r_mcangle_it 1.655 r_mcangle_other 1.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.252 r_dihedral_angle_4_deg 15.471 r_dihedral_angle_3_deg 12.709 r_dihedral_angle_1_deg 6.776 r_lrange_it 3.201 r_lrange_other 3.155 r_scangle_other 1.926 r_scangle_it 1.917 r_mcangle_it 1.655 r_mcangle_other 1.654 r_scbond_it 1.301 r_angle_refined_deg 1.276 r_scbond_other 1.226 r_angle_other_deg 1.167 r_mcbond_it 1.059 r_mcbond_other 1.054 r_symmetry_nbd_refined 0.191 r_nbd_other 0.186 r_nbd_refined 0.179 r_symmetry_nbd_other 0.167 r_nbtor_refined 0.145 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.091 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.048 r_bond_refined_d 0.004 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 1849 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing