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Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other TrRosetta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.5, 35% w/v PAA 2100
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.147 α = 90 b = 86.147 β = 90 c = 234.105 γ = 120
Symmetry Space Group P 65 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 EIGER2 XE 16M 2020-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.36 78.04 100 1 22.3 113.8 22089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.45 0.306
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 TrRosetta 2.36 74.717 21957 1097 99.524 0.206 0.2036 0.2038 0.2576 0.259
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] 0.762 0.381 0.762 -2.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 15.422 r_lrange_it 12.771 r_lrange_other 12.77 r_scangle_it 10.478 r_scangle_other 10.478 r_mcangle_it 9.338 r_mcangle_other 9.336 r_scbond_it 7.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 15.422 r_lrange_it 12.771 r_lrange_other 12.77 r_scangle_it 10.478 r_scangle_other 10.478 r_mcangle_it 9.338 r_mcangle_other 9.336 r_scbond_it 7.751 r_scbond_other 7.705 r_dihedral_angle_1_deg 7.038 r_mcbond_other 6.993 r_mcbond_it 6.991 r_angle_other_deg 2.327 r_angle_refined_deg 1.528 r_symmetry_nbd_refined 0.243 r_nbd_other 0.229 r_symmetry_nbd_other 0.221 r_nbd_refined 0.196 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_other_d 0.035 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3245 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PHENIX model building PHASER phasing xia2 data scaling xia2 data reduction