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Structure of R175A S. cerevisiae Fdc1 with prFMN in the iminium form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M sodium cacodylate pH 6.5, 0.25M Calcium Acetate, 15% PEG 4k
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.48 α = 90 b = 98.64 β = 97.24 c = 118.17 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 2015-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 .928 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 77.89 100 5.52 3.4 167153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.134 1.071 2.9
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 4ZAC 2.05 77.89 158817 8336 99.7 0.1848 0.18265 0.1908 0.22602 0.2298 RANDOM 27.333
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 -1.47 2.29 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.835 r_dihedral_angle_4_deg 19.794 r_dihedral_angle_3_deg 14.88 r_dihedral_angle_1_deg 6.573 r_long_range_B_refined 5.845 r_long_range_B_other 5.764 r_scangle_other 4.374 r_scbond_other 2.827 r_scbond_it 2.826 r_mcangle_it 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.835 r_dihedral_angle_4_deg 19.794 r_dihedral_angle_3_deg 14.88 r_dihedral_angle_1_deg 6.573 r_long_range_B_refined 5.845 r_long_range_B_other 5.764 r_scangle_other 4.374 r_scbond_other 2.827 r_scbond_it 2.826 r_mcangle_it 2.814 r_mcangle_other 2.814 r_mcbond_it 1.936 r_mcbond_other 1.935 r_angle_refined_deg 1.874 r_angle_other_deg 1.109 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 15534 Nucleic Acid Atoms Solvent Atoms 1245 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing