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Crystal structure of deep network hallucinated protein 0738_mod
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other computational model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293.15 Protein concentration: 3.7 mg/mL
Sample buffer:20 mM HEPES, 50 mM NaCl, pH 7.4
Crystallants: 40% v/v pentaerythritol propoxylate (5/4 PO/OH), 15% v/v ethanol
Crystal Properties Matthews coefficient Solvent content 1.91 35.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.291 α = 90 b = 46.291 β = 90 c = 82.492 γ = 120
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 2021-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 2.4 50 99.8 0.08 0.03 0.999 18 10.7 7742 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.856 2.6 8.2
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 computational model 2.4 40.09 2 7132 363 92.16 0.2211 0.2189 0.2202 0.2601 0.2558 41.24
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 12.2182 f_angle_d 0.4299 f_chiral_restr 0.0401 f_plane_restr 0.0036 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement ADSC data collection autoPROC data processing SCALEPACK data scaling PHASER phasing HKL-2000 data reduction