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Structure of T. atroviride variant TaFdcV in complex with prFMN-butynoic acid adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Potassium thiocyanate, sodium bromide, MES, PEG Smear High (BCS screen from Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.647 α = 90 b = 74.647 β = 90 c = 345.752 γ = 120
Symmetry Space Group P 32 2 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 PILATUS3 6M 2018-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.77 64.65 100 0.9 6.8 9.1 110826
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 1.77 1.8 98.7 0.5 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EV4 1.77 64.65 105229 5472 99.93 0.17663 0.17511 0.1843 0.20604 0.2115 RANDOM 22.445
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.551 r_dihedral_angle_4_deg 21.029 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_1_deg 6.693 r_long_range_B_refined 5.227 r_long_range_B_other 5.199 r_scangle_other 4.35 r_scbond_it 2.952 r_scbond_other 2.952 r_mcangle_it 2.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.551 r_dihedral_angle_4_deg 21.029 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_1_deg 6.693 r_long_range_B_refined 5.227 r_long_range_B_other 5.199 r_scangle_other 4.35 r_scbond_it 2.952 r_scbond_other 2.952 r_mcangle_it 2.398 r_mcangle_other 2.398 r_mcbond_it 1.814 r_mcbond_other 1.81 r_angle_refined_deg 1.716 r_angle_other_deg 1.414 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 7639 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing