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Cell wall anchoring domain of the surface layer protein of Methanococcus voltae (aa 24-75; 484-576)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 JCSG+ eco condition C2
1.0 M LiCl, 0.1 M citrate pH 4.0, 20 % PEG 6000
0.3 ul condition + 0.3 ul protein solution
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.34 α = 90 b = 53.268 β = 90 c = 55.627 γ = 90
Symmetry Space Group P 2 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 Bruker PHOTON III 2024-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 70 kV 1.3414
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 2.05 46.34 90.7 0.332 0.996 8.2 23.5 4977
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 2.05 2.24 70.1 1.8 0.65 1.6 15.8
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 2.05 46.34 4974 286 54.725 0.266 0.2652 0.2653 0.2825 0.2829 22.898
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] -1.316 0.554 0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.16 r_dihedral_angle_6_deg 16.086 r_lrange_it 8.812 r_lrange_other 8.812 r_dihedral_angle_1_deg 6.047 r_scangle_it 3.552 r_scangle_other 3.549 r_mcangle_it 3.505 r_mcangle_other 3.504 r_dihedral_angle_2_deg 3.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.16 r_dihedral_angle_6_deg 16.086 r_lrange_it 8.812 r_lrange_other 8.812 r_dihedral_angle_1_deg 6.047 r_scangle_it 3.552 r_scangle_other 3.549 r_mcangle_it 3.505 r_mcangle_other 3.504 r_dihedral_angle_2_deg 3.029 r_mcbond_it 2.109 r_mcbond_other 2.107 r_scbond_it 2.054 r_scbond_other 2.052 r_angle_refined_deg 1.075 r_angle_other_deg 0.358 r_nbd_other 0.31 r_symmetry_nbd_refined 0.215 r_nbd_refined 0.205 r_symmetry_nbd_other 0.205 r_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.168 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.044 r_bond_refined_d 0.006 r_gen_planes_refined 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 928 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction STARANISO data scaling PHASER phasing