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Crystal structure of the second StART-like domain from Arabidopsis C2 and GRAM domain-containing (C2GR) protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Bicine & Tris (pH 8.5), 12.5% MPD, 12.5% PEG1000, and 12% PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.234 α = 90 b = 69.797 β = 90 c = 77.364 γ = 90
Symmetry Space Group C 2 2 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 2021-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 50 98.3 0.065 0.996 28.53 8.2 19927
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 1.7 1.76 0.896
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.704 31.812 19907 910 98.248 0.198 0.1964 0.2062 0.2325 0.2397 32.035
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] 0.521 1.338 -1.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.557 r_lrange_other 14.281 r_lrange_it 14.272 r_dihedral_angle_3_deg 13.081 r_scangle_it 8.556 r_scangle_other 8.552 r_dihedral_angle_1_deg 6.706 r_dihedral_angle_2_deg 5.987 r_mcangle_it 5.677 r_mcangle_other 5.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.557 r_lrange_other 14.281 r_lrange_it 14.272 r_dihedral_angle_3_deg 13.081 r_scangle_it 8.556 r_scangle_other 8.552 r_dihedral_angle_1_deg 6.706 r_dihedral_angle_2_deg 5.987 r_mcangle_it 5.677 r_mcangle_other 5.676 r_scbond_it 5.556 r_scbond_other 5.553 r_mcbond_it 3.818 r_mcbond_other 3.818 r_angle_refined_deg 1.59 r_angle_other_deg 0.57 r_symmetry_nbd_other 0.204 r_nbd_other 0.193 r_nbtor_refined 0.183 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.096 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_refined 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_ext_dist_refined_b 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1463 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing