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Crystal Structure of LM2363
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other de novo design model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH 7.5, and 30% (v/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.913 α = 90 b = 60.913 β = 90 c = 96.608 γ = 120
Symmetry Space Group P 63 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 PILATUS3 2M 2023-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00002 ALS 8.2.1
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 1.95 46.3 100 0.716 0.16 0.981 6.9 23.8 8265 31.35
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 1.95 2 100 1.471 0.309 0.798 2.2 24.1
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 1.95 46.3 1.43 8241 813 99.88 0.2464 0.2414 0.2417 0.2913 0.2933 40.49
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 20.8096 f_angle_d 0.7589 f_chiral_restr 0.0537 f_bond_d 0.0063 f_plane_restr 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing