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Crystal structure of ClAgl29B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 0.1 M sodium citrate (pH 3.5), 5% PEG 20,000, 5% 2-propanol
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.132 α = 90 b = 123.405 β = 90 c = 166.605 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 2M 2021-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.609 99.165 99.5 0.063 0.069 0.999 22.17 6.7 194275 22.3
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 1.61 1.71 97 0.423 0.459 0.942 4.51 6.6
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 AlphaFold2 model 1.609 45.418 194274 9719 99.483 0.173 0.1722 0.185 0.1884 0.1998 18.001
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] 1.04 -0.245 -0.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.334 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_2_deg 9.784 r_dihedral_angle_1_deg 6.649 r_lrange_it 4.961 r_lrange_other 4.734 r_scangle_it 3.488 r_scangle_other 3.488 r_mcangle_it 2.496 r_mcangle_other 2.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.334 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_2_deg 9.784 r_dihedral_angle_1_deg 6.649 r_lrange_it 4.961 r_lrange_other 4.734 r_scangle_it 3.488 r_scangle_other 3.488 r_mcangle_it 2.496 r_mcangle_other 2.496 r_scbond_it 2.275 r_scbond_other 2.275 r_mcbond_it 1.665 r_mcbond_other 1.663 r_angle_refined_deg 1.364 r_angle_other_deg 0.472 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.223 r_nbd_other 0.207 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.107 r_ncsr_local_group_1 0.086 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.07 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8828 Nucleic Acid Atoms Solvent Atoms 1008 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing