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Crystal structure of DNPH1 bound by compound 39.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Non-public structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25 % PEG3350, 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.85 33.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.134 α = 91.78 b = 39.877 β = 100.11 c = 48.418 γ = 114.85
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 PILATUS 6M 2024-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97629 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.217 35.94 75.4 0.997 8.8 1.7 39210
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 1.22 1.38 0.283
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.217 17.57 39190 1887 53 0.1819 0.18 0.2192 0.23 RANDOM 13.2
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] -0.0722 0.3872 0.2797 -0.0627 -0.3939 0.1349
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.03 t_omega_torsion 4.16 t_angle_deg 1.19 t_bond_d 0.013 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2160 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 82
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHASER phasing