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Crystal structure of monomeric FICD mutant L258D complexed with MgATP
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 293 1.0 M Sodium Chloride; 10% Ethanol
Crystal Properties Matthews coefficient Solvent content 4.96 75.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.842 α = 90 b = 186.842 β = 90 c = 76.844 γ = 120
Symmetry Space Group P 64 2 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 PILATUS3 6M 2018-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.54 93.42 100 0.167 0.178 0.06 0.999 13 16.1 26617
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 2.54 2.65 100 1.009 1.073 0.364 0.503 2.5 16.5
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 2.54 93.42 25190 1384 99.98 0.23356 0.23254 0.2335 0.25206 0.2527 RANDOM 58.033
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] 1.22 0.61 1.22 -3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.723 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 14.594 r_dihedral_angle_1_deg 4.691 r_long_range_B_refined 4.037 r_long_range_B_other 4.036 r_mcangle_it 2.046 r_mcangle_other 2.045 r_scangle_other 1.886 r_mcbond_it 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.723 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 14.594 r_dihedral_angle_1_deg 4.691 r_long_range_B_refined 4.037 r_long_range_B_other 4.036 r_mcangle_it 2.046 r_mcangle_other 2.045 r_scangle_other 1.886 r_mcbond_it 1.146 r_mcbond_other 1.146 r_angle_refined_deg 1.13 r_angle_other_deg 1.06 r_scbond_it 1.032 r_scbond_other 1.032 r_chiral_restr 0.036 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 2680 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing