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NatL2 in complex with two molecules of salicylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M KSCN, 0.1 M sodium citrate pH 6, 24-32% PEG MME 2K
Crystal Properties Matthews coefficient Solvent content 2.51 50.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.46 α = 90 b = 139.24 β = 90 c = 129.66 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 PILATUS3 6M 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.89 71.13 100 0.119 0.997 9.4 6.5 77807
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 1.89 1.94 100 1.628 0.65 1.3 6.7
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 FREE R-VALUE 6SIW 1.89 71.128 77773 3811 99.949 0.199 0.1978 0.2086 0.2303 0.2372 47.313
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] -2.732 3.626 -0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.437 r_dihedral_angle_4_deg 21.446 r_dihedral_angle_3_deg 14.626 r_dihedral_angle_1_deg 6.974 r_lrange_other 5.323 r_lrange_it 5.322 r_scangle_it 3.478 r_scangle_other 3.478 r_mcangle_it 2.734 r_mcangle_other 2.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.437 r_dihedral_angle_4_deg 21.446 r_dihedral_angle_3_deg 14.626 r_dihedral_angle_1_deg 6.974 r_lrange_other 5.323 r_lrange_it 5.322 r_scangle_it 3.478 r_scangle_other 3.478 r_mcangle_it 2.734 r_mcangle_other 2.734 r_scbond_it 2.196 r_scbond_other 2.195 r_mcbond_it 1.795 r_mcbond_other 1.792 r_angle_refined_deg 1.563 r_angle_other_deg 1.306 r_nbd_other 0.218 r_symmetry_xyhbond_nbd_refined 0.205 r_nbd_refined 0.193 r_symmetry_nbd_other 0.18 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.095 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_metal_ion_refined 0.056 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6727 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing