☰ Navigation Tabs
Crystal structure of human DNPH1 bound to inhibitor 1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 292 25.1% (w/v) PEG 3350, 2.73% (v/v) Methanol and Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 1.95 36.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.761 α = 90 b = 64.833 β = 90 c = 128.48 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2023-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.92 NSLS-II 17-ID-2
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 1.47 22.82 99.7 0.083 0.088 0.028 0.998 14.8 9.4 43023
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 1.47 1.5 94.4 0.776 0.82 0.261 0.846 9.4
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 1.47 22.82 1.34 42971 2192 99.62 0.1545 0.1532 0.1534 0.1786 0.1789
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 10.92 f_angle_d 1.182 f_chiral_restr 0.081 f_plane_restr 0.016 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2016 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing