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Crystal structure of ClAgl29A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M sodium citrate (pH 5.5), 16% PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.577 α = 90 b = 95.521 β = 97.331 c = 83.55 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2020-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 82.9 98.9 0.08 0.09 0.999 14.8 7 76908 42.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 97.3 0.89 0.96 0.9 2.45
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 2XSD 2.006 47.806 76891 3855 98.848 0.207 0.2046 0.2123 0.2427 0.2455 44.108
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] -2.669 -1.326 7.172 -4.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.605 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_1_deg 6.972 r_dihedral_angle_2_deg 6.646 r_lrange_other 5.764 r_lrange_it 5.763 r_scangle_it 4.209 r_scangle_other 4.209 r_mcangle_it 3.944 r_mcangle_other 3.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.605 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_1_deg 6.972 r_dihedral_angle_2_deg 6.646 r_lrange_other 5.764 r_lrange_it 5.763 r_scangle_it 4.209 r_scangle_other 4.209 r_mcangle_it 3.944 r_mcangle_other 3.944 r_scbond_it 2.693 r_scbond_other 2.693 r_mcbond_it 2.568 r_mcbond_other 2.563 r_angle_refined_deg 1.082 r_angle_other_deg 0.381 r_metal_ion_refined 0.199 r_nbd_refined 0.197 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.182 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.126 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.055 r_ncsr_local_group_1 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8634 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing