☰ Navigation Tabs
N-Terminal Domain of CRISPR-associated DinG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 Mother liquor consisted of 18% PEG 3350, 0.1M Na citrate buffer (pH 4.0), and 0.2M Ammonium Sulfate. Mother liquor was mixed with concentrated protein (12 mg/ml) at a ratio of 2:1.5 (protein solution : ML)
Crystal Properties Matthews coefficient Solvent content 2.146137 42.72334
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.669 α = 90 b = 39.304 β = 95.045 c = 83.097 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 IMAGE PLATE RIGAKU RAXIS IV++ 2024-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.55 26.87 73.27 0.06 0.073 0.041 0.997 21.1 2.9 18483 10.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 5.45 0.23 0.326 0.23 0.921 1.3 1.09
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 1.55 26.87 1.38 18481 904 73.27 0.1334 0.1319 0.132 0.1617 0.1617 15.6
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 13.6247 f_angle_d 0.9599 f_chiral_restr 0.0508 f_plane_restr 0.0108 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 703 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing Aimless data scaling pointless data scaling DIALS data reduction HKL-3000 data collection