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Structure of in silico modelled artificial Maquette-3 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other in silico Maquette model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM HEPES, 1.5 M Potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.69 α = 89.86 b = 65.9 β = 90.29 c = 68.26 γ = 117.36
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 2019-07-13 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 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 1.85 30 97.5 0.051 11.3 3.4 80776
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 1.85 1.95 98.5 0.545 2.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT in silico Maquette model 1.85 30 76730 4038 97.52 0.1886 0.1893 0.1948 0.2234 0.237 RANDOM 41.218
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] 1.83 0.7 0.93 -1.18 0.12 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.86 r_dihedral_angle_3_deg 13.897 r_dihedral_angle_4_deg 12.107 r_dihedral_angle_1_deg 3.417 r_angle_other_deg 1.165 r_angle_refined_deg 1.096 r_rigid_bond_restr 0.776 r_chiral_restr 0.054 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.86 r_dihedral_angle_3_deg 13.897 r_dihedral_angle_4_deg 12.107 r_dihedral_angle_1_deg 3.417 r_angle_other_deg 1.165 r_angle_refined_deg 1.096 r_rigid_bond_restr 0.776 r_chiral_restr 0.054 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6488 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing