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F420-1/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 2PHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-1
Crystal Properties Matthews coefficient Solvent content 2.01 38.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.082 α = 90 b = 69.082 β = 90 c = 92.352 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 2018-03-28 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 1.7 48.9 100 0.019 0.998 18.2 26.7 25326
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 1.7 1.73 100 0.653 0.538 1.5 27.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PHN 1.7 48.896 25283 1274 99.968 0.211 0.2097 0.2148 0.2337 0.2394 RANDOM 35.915
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] -0.018 -0.018 0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.98 r_dihedral_angle_4_deg 19.14 r_dihedral_angle_3_deg 11.776 r_dihedral_angle_1_deg 6.71 r_lrange_it 3.305 r_lrange_other 3.262 r_angle_other_deg 2.987 r_scangle_it 2.241 r_scangle_other 2.24 r_mcangle_it 1.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.98 r_dihedral_angle_4_deg 19.14 r_dihedral_angle_3_deg 11.776 r_dihedral_angle_1_deg 6.71 r_lrange_it 3.305 r_lrange_other 3.262 r_angle_other_deg 2.987 r_scangle_it 2.241 r_scangle_other 2.24 r_mcangle_it 1.889 r_mcangle_other 1.888 r_scbond_it 1.43 r_scbond_other 1.418 r_angle_refined_deg 1.31 r_mcbond_it 1.217 r_mcbond_other 1.215 r_symmetry_xyhbond_nbd_other 0.266 r_nbd_other 0.189 r_symmetry_nbd_refined 0.179 r_nbd_refined 0.175 r_symmetry_nbd_other 0.168 r_symmetry_xyhbond_nbd_refined 0.156 r_nbtor_refined 0.145 r_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.047 r_bond_other_d 0.036 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1856 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing