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Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with FMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.1 M Tris/BICINE buffer pH 8.5, 20% v/v ethylene glycol and 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.91 α = 90 b = 139.25 β = 93.74 c = 136.88 γ = 90
Symmetry Space Group P 1 21 1
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-F 2016-02-17 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 2.66 74.2 99.8 0.144 1 9.8 3.8 343818
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 2.66 2.73 99.8 1.103 0.5 1.6 3.8
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.66 74.2 86650 4311 99.78 0.20097 0.1992 0.23599 0.2051 RANDOM 55.86
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] 3.24 -0.68 -3.19 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.679 r_dihedral_angle_4_deg 19.191 r_dihedral_angle_3_deg 17.685 r_long_range_B_refined 9.974 r_long_range_B_other 9.974 r_scangle_other 6.956 r_dihedral_angle_1_deg 6.23 r_mcangle_it 5.891 r_mcangle_other 5.891 r_scbond_other 4.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.679 r_dihedral_angle_4_deg 19.191 r_dihedral_angle_3_deg 17.685 r_long_range_B_refined 9.974 r_long_range_B_other 9.974 r_scangle_other 6.956 r_dihedral_angle_1_deg 6.23 r_mcangle_it 5.891 r_mcangle_other 5.891 r_scbond_other 4.431 r_scbond_it 4.43 r_mcbond_it 3.74 r_mcbond_other 3.738 r_angle_refined_deg 1.58 r_angle_other_deg 0.968 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 20433 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MLPHARE phasing