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Crystal structure of the engineered photoenzyme VEnT1.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M MIB pH = 7 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.89 35.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.729 α = 90 b = 73.437 β = 94.163 c = 74.121 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 DECTRIS EIGER2 XE 16M 2024-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.52 50.6 95 0.09754 0.0402 0.998 13.12 6.7 79341 19.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.56 65.04 1.671 0.8539 0.372 1.26 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.52 50.6 1.36 79199 1868 95 0.1443 0.1435 0.1483 0.1744 0.1777 25.54
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 15.5087 f_angle_d 1.0107 f_chiral_restr 0.0647 f_plane_restr 0.0109 f_bond_d 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2616 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 2224
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing