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Structure of E285D S. cerevisiae Fdc1 with prFMN in the hydroxylated 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 2.81 56.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.1 α = 90 b = 96.82 β = 96.61 c = 116.78 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 2013-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 .979 Diamond I02
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 2.06 34.35 99 8.35 2.9 154138
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 2.06 3.134 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 2.06 34.35 146617 7522 98.83 0.16965 0.16743 0.1763 0.21273 0.2191 RANDOM 28.91
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] -0.95 -1.3 1.51 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.849 r_dihedral_angle_4_deg 20 r_dihedral_angle_3_deg 14.388 r_dihedral_angle_1_deg 6.676 r_long_range_B_refined 5.965 r_long_range_B_other 5.869 r_scangle_other 4.651 r_scbond_it 3.049 r_scbond_other 3.049 r_mcangle_it 2.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.849 r_dihedral_angle_4_deg 20 r_dihedral_angle_3_deg 14.388 r_dihedral_angle_1_deg 6.676 r_long_range_B_refined 5.965 r_long_range_B_other 5.869 r_scangle_other 4.651 r_scbond_it 3.049 r_scbond_other 3.049 r_mcangle_it 2.853 r_mcangle_other 2.853 r_mcbond_it 2.053 r_mcbond_other 2.053 r_angle_refined_deg 1.821 r_angle_other_deg 1.083 r_chiral_restr 0.107 r_bond_refined_d 0.016 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 15678 Nucleic Acid Atoms Solvent Atoms 1308 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing