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Self assembly domain of the surface layer protein of Viridibacillus arvi (aa 765-844)
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 7.5 293 JCSG+ eco, condition G10
0.15 M KBr, 30 % PEG 2000 MME
22 g/l protein in 25 mM HEPES pH 7.5, 150 mM NaCl
0.3 ul condition + 0.3 ul protein
Crystal Properties Matthews coefficient Solvent content 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.017 α = 90 b = 35.049 β = 91.234 c = 68.017 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 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 2.1 48.66 99.83 0.1155 0.994 9.3 6 19156 30.19
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 2.175 0.8077 0.589 1.4
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 2.1 48.658 19155 900 99.911 0.204 0.201 0.2011 0.2599 0.2587 37.483
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] -0.828 -0.534 0.696 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.745 r_dihedral_angle_3_deg 14.217 r_dihedral_angle_1_deg 7.972 r_lrange_it 6.243 r_lrange_other 6.17 r_scangle_it 3.338 r_scangle_other 3.337 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 2.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.745 r_dihedral_angle_3_deg 14.217 r_dihedral_angle_1_deg 7.972 r_lrange_it 6.243 r_lrange_other 6.17 r_scangle_it 3.338 r_scangle_other 3.337 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 2.167 r_scbond_other 2.166 r_mcbond_it 1.812 r_mcbond_other 1.809 r_angle_refined_deg 1.386 r_angle_other_deg 0.462 r_symmetry_xyhbond_nbd_refined 0.227 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.213 r_nbd_other 0.201 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.171 r_nbtor_refined 0.165 r_ncsr_local_group_6 0.125 r_ncsr_local_group_2 0.121 r_ncsr_local_group_5 0.109 r_ncsr_local_group_1 0.099 r_ncsr_local_group_4 0.094 r_ncsr_local_group_3 0.09 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.076 r_chiral_restr 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 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 2535 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction pointless data scaling PHASER phasing