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Crystal structure of dimeric FICD mutant K256S
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 8.5 293 0.1 M Tris pH 8.5; 0.05 M Magnesium Chloride; 40% Ethanol
Crystal Properties Matthews coefficient Solvent content 2.84 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.815 α = 90 b = 76.508 β = 90 c = 131.972 γ = 90
Symmetry Space Group P 2 21 21
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 2017-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97942 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 2.25 65.99 99.9 0.109 0.136 0.079 0.993 6.8 4.4 21825
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 2.25 2.32 99.5 0.385 0.488 0.295 0.547 2.4 4.4
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 2.25 65.99 20678 1098 99.83 0.21009 0.20763 0.2154 0.25863 0.2655 RANDOM 42.468
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] 1.42 -0.16 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.961 r_dihedral_angle_4_deg 14.07 r_dihedral_angle_3_deg 13.74 r_long_range_B_refined 5.761 r_long_range_B_other 5.603 r_dihedral_angle_1_deg 4.999 r_scangle_other 3.436 r_mcangle_it 3.068 r_mcangle_other 3.067 r_scbond_it 2.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.961 r_dihedral_angle_4_deg 14.07 r_dihedral_angle_3_deg 13.74 r_long_range_B_refined 5.761 r_long_range_B_other 5.603 r_dihedral_angle_1_deg 4.999 r_scangle_other 3.436 r_mcangle_it 3.068 r_mcangle_other 3.067 r_scbond_it 2.018 r_scbond_other 2.018 r_mcbond_it 1.861 r_mcbond_other 1.861 r_angle_other_deg 1.188 r_angle_refined_deg 1.18 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 2640 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing