☰ Navigation Tabs
Structure of an evolved dimeric form of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with prFMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.12 M alcohols, 0.1 M NaHEPES/MOPS buffer pH 7.5, 20% v/v ethylene glycol and 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.72 α = 90 b = 63.93 β = 90 c = 98.3 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 100 PIXEL DECTRIS PILATUS 6M 2016-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.08 83.86 97.3 0.07 1 12.1 4.5 279066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.13 98.1 0.92 0.6 1.7 4.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H6V 2.25 83.86 46764 2470 96.49 0.19667 0.19395 0.24772 0.2507 RANDOM 53.524
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] -0.02 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.084 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 16.604 r_long_range_B_refined 10.821 r_long_range_B_other 10.82 r_scangle_other 8.246 r_mcangle_it 7.088 r_mcangle_other 7.087 r_dihedral_angle_1_deg 6.547 r_scbond_it 5.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.084 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 16.604 r_long_range_B_refined 10.821 r_long_range_B_other 10.82 r_scangle_other 8.246 r_mcangle_it 7.088 r_mcangle_other 7.087 r_dihedral_angle_1_deg 6.547 r_scbond_it 5.397 r_scbond_other 5.396 r_mcbond_it 4.874 r_mcbond_other 4.871 r_angle_refined_deg 1.91 r_angle_other_deg 1.114 r_chiral_restr 0.221 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6494 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing