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De Novo Design of membrane protein--mini-eVgL membrane protein, C2221 form-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MPW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.2 M (NH4)2SO4, 0.1 M Na Acet pH 4.6, 28 %v/v PEG MME 550
Crystal Properties Matthews coefficient Solvent content 1.8 31.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.55 α = 90 b = 81.89 β = 90 c = 47.84 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M 2018-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.38 50 92.7 0.157 0.165 0.998 9.45 11.68 4274 54.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.53 53.5 1.73 1.87 0.877 3.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6MPW 2.5 33.147 1.36 7235 357 98.97 0.2139 0.2129 0.2153 0.2341 0.2323
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.446 f_angle_d 0.494 f_chiral_restr 0.036 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1031 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing