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Structure of A. niger Fdc T395M variant (AnFdcI) in complex with prFMN
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 BIS-TRIS propane, potassium thiocyanate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.91 α = 90 b = 63.85 β = 90 c = 87.82 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2018-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.1 42.09 97.9 1 15.7 4.9 213550
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 1.1 1.12 0.3 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 1.1 42.09 202756 10735 97.89 0.15886 0.15818 0.1678 0.17163 0.1824 RANDOM 11.888
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.127 r_dihedral_angle_4_deg 20.041 r_dihedral_angle_3_deg 12.069 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 3.95 r_long_range_B_other 3.795 r_scangle_other 3.283 r_scbond_other 2.233 r_scbond_it 2.231 r_angle_refined_deg 2.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.127 r_dihedral_angle_4_deg 20.041 r_dihedral_angle_3_deg 12.069 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 3.95 r_long_range_B_other 3.795 r_scangle_other 3.283 r_scbond_other 2.233 r_scbond_it 2.231 r_angle_refined_deg 2.019 r_mcangle_other 1.575 r_angle_other_deg 1.573 r_mcangle_it 1.572 r_mcbond_it 1.101 r_mcbond_other 1.093 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.018 r_gen_planes_other 0.002 r_bond_other_d 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 3867 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing