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Crystal structure of K74A mutant of Cap4 SAVED domain-containing receptor from Enterobacter cloacae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Bis-Tris propane pH 6.5, 0.2 M sodium acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.901 α = 90 b = 70.212 β = 90 c = 150.734 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 CCD RAYONIX MX300-HS 2021-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.42 30 98.1 0.06 28.7 6.9 23087
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 99.5 0.653 2.1 5.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7YIB 2.428 29.895 20808 1033 88.308 0.203 0.2019 0.2056 0.2192 0.2182 41.116
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] 0.639 -0.602 -0.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.785 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 15.647 r_lrange_other 9.14 r_lrange_it 9.137 r_dihedral_angle_1_deg 8.298 r_mcangle_it 6.403 r_mcangle_other 6.401 r_scangle_it 6.366 r_scangle_other 6.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.785 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 15.647 r_lrange_other 9.14 r_lrange_it 9.137 r_dihedral_angle_1_deg 8.298 r_mcangle_it 6.403 r_mcangle_other 6.401 r_scangle_it 6.366 r_scangle_other 6.366 r_mcbond_other 4.102 r_mcbond_it 4.101 r_scbond_it 4.072 r_scbond_other 4.071 r_angle_refined_deg 1.414 r_angle_other_deg 1.226 r_nbd_other 0.255 r_nbd_refined 0.205 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.168 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.06 r_symmetry_xyhbond_nbd_other 0.051 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3915 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing