☰ Navigation Tabs
Crystal structure of dimeric wild type FICD complexed with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Tris pH 7.5; 20% PEG 300; 5% PEG8K; 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.55 65.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.671 α = 90 b = 107.652 β = 90 c = 132.597 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-F 2017-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.7 83.58 100 0.163 0.195 0.104 0.996 6 6.4 31293
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 0.717 0.851 0.456 0.72 1.8 6.5
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 4u0u 2.7 83.58 29763 1497 99.98 0.28458 0.28291 0.2813 0.31868 0.32 RANDOM 54.904
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] -2.34 6.56 -4.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.227 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_4_deg 13.225 r_long_range_B_refined 5.055 r_long_range_B_other 5.023 r_dihedral_angle_1_deg 4.598 r_mcangle_it 1.745 r_mcangle_other 1.744 r_scangle_other 1.307 r_angle_refined_deg 1.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.227 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_4_deg 13.225 r_long_range_B_refined 5.055 r_long_range_B_other 5.023 r_dihedral_angle_1_deg 4.598 r_mcangle_it 1.745 r_mcangle_other 1.744 r_scangle_other 1.307 r_angle_refined_deg 1.143 r_angle_other_deg 1.027 r_mcbond_it 0.961 r_mcbond_other 0.961 r_scbond_it 0.684 r_scbond_other 0.684 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 5362 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing