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Crystal Structure of the Coxiella burnetii E110Q Mutant 2-methylisocitrate lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 292 10% v/v EtOH, 0.1 M sodium-citrate pH 4.2, 1% w/w PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.13 42.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.18 α = 90 b = 74.18 β = 90 c = 184.45 γ = 120
Symmetry Space Group P 31 2 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 PILATUS3 6M 2024-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.82 61.48 96.4 0.9952 13.32 8.7 51772
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.3443
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.82 61.48 48649 2593 95.44 0.2355 0.23211 0.2321 0.29889 0.2988 RANDOM 55.033
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] 0.85 0.42 0.85 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_long_range_B_refined 16.499 r_dihedral_angle_3_deg 15.674 r_dihedral_angle_4_deg 13.658 r_scbond_it 12.887 r_mcangle_it 12.404 r_mcbond_it 10.502 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.475 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_long_range_B_refined 16.499 r_dihedral_angle_3_deg 15.674 r_dihedral_angle_4_deg 13.658 r_scbond_it 12.887 r_mcangle_it 12.404 r_mcbond_it 10.502 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.475 r_chiral_restr 0.118 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4475 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing