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Crystal structure of the first StART-like domain of Arabidopsis C2 and GRAM domain-containing (C2GR) protein in apo form
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 NaAc (pH 4.6) and 1.8 M MgSO4
Crystal Properties Matthews coefficient Solvent content 2.61 52.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.847 α = 90 b = 87.847 β = 90 c = 122.94 γ = 120
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 2020-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
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 2.097 50 100 0.111 0.997 25.52 13.4 31514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 1.489 0.623
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 2.097 47.813 29284 1508 93.033 0.239 0.2376 0.2413 0.2575 0.2571 33.681
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] 0.127 0.127 -0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.704 r_dihedral_angle_3_deg 11.957 r_lrange_it 10.332 r_lrange_other 10.306 r_dihedral_angle_1_deg 7.365 r_scangle_it 6.724 r_scangle_other 6.723 r_mcangle_it 6.549 r_mcangle_other 6.548 r_dihedral_angle_2_deg 5.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.704 r_dihedral_angle_3_deg 11.957 r_lrange_it 10.332 r_lrange_other 10.306 r_dihedral_angle_1_deg 7.365 r_scangle_it 6.724 r_scangle_other 6.723 r_mcangle_it 6.549 r_mcangle_other 6.548 r_dihedral_angle_2_deg 5.756 r_scbond_it 4.526 r_scbond_other 4.525 r_mcbond_it 4.362 r_mcbond_other 4.348 r_angle_refined_deg 1.737 r_angle_other_deg 0.583 r_nbd_other 0.339 r_symmetry_nbd_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.199 r_nbd_refined 0.18 r_symmetry_nbd_other 0.18 r_ncsr_local_group_1 0.174 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 2776 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing