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Stopper protein of phage 812 in closed conformation
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, HANGING DROP 8 293.15 1.6 M NaCl, 8% PEG 6000, 20% glycerol, 3% dextran sulphate sodium
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.366 α = 90 b = 93.366 β = 90 c = 122.531 γ = 120
Symmetry Space Group P 6 2 2
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 6M 2017-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 37.2 99.9 0.13 23.26 11.7 16664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.8 0.689 4.21
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 2.2 37.159 16649 1632 99.844 0.193 0.19 0.1982 0.2192 0.227 31.435
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] -1.375 -0.687 -1.375 4.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.971 r_dihedral_angle_3_deg 11.68 r_lrange_it 6.621 r_lrange_other 6.546 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.721 r_scangle_other 4.719 r_mcangle_it 3.431 r_mcangle_other 3.43 r_dihedral_angle_2_deg 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.971 r_dihedral_angle_3_deg 11.68 r_lrange_it 6.621 r_lrange_other 6.546 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.721 r_scangle_other 4.719 r_mcangle_it 3.431 r_mcangle_other 3.43 r_dihedral_angle_2_deg 3.017 r_scbond_it 2.798 r_scbond_other 2.796 r_mcbond_it 2.129 r_mcbond_other 2.128 r_dihedral_angle_other_3_deg 2.014 r_angle_refined_deg 1.223 r_angle_other_deg 0.393 r_symmetry_nbd_other 0.217 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.179 r_nbd_other 0.178 r_symmetry_nbd_refined 0.168 r_symmetry_xyhbond_nbd_other 0.153 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1815 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing