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Crystal structure of monomeric FICD mutant L258D complexed with MgAMP-PNP
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 1.5 M Sodium Chloride; 10% Ethanol
Crystal Properties Matthews coefficient Solvent content 4.95 75.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.358 α = 90 b = 186.358 β = 90 c = 77.1 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 2.31 93.18 99.4 0.071 0.089 0.054 0.998 10.3 4.6 34573
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 2.31 2.39 99.1 0.611 0.771 0.465 0.523 1.8 4.6
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 2.32 93.18 32586 1660 98.98 0.21635 0.21453 0.2185 0.25095 0.2516 RANDOM 56.459
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] 0.71 0.36 0.71 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.367 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 14.491 r_long_range_B_refined 6.789 r_long_range_B_other 6.703 r_dihedral_angle_1_deg 5.21 r_scangle_other 4.191 r_mcangle_it 3.528 r_mcangle_other 3.528 r_scbond_it 2.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.367 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 14.491 r_long_range_B_refined 6.789 r_long_range_B_other 6.703 r_dihedral_angle_1_deg 5.21 r_scangle_other 4.191 r_mcangle_it 3.528 r_mcangle_other 3.528 r_scbond_it 2.415 r_scbond_other 2.415 r_mcbond_it 2.118 r_mcbond_other 2.104 r_angle_refined_deg 1.173 r_angle_other_deg 1.124 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 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 2693 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing