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Crystal structure of human DNPH1 mutant-Y24F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.2 M ammonium sulfate, 0.1 M MES pH 6.5 30 % PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 1.94 36.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.907 α = 90 b = 139.907 β = 90 c = 33.313 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 X 9M 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 2.14 70.03 100 0.186 0.206 0.088 0.996 7.7 10.4 13475
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 2.14 2.2 100 1.028 0.493 0.885 2.1 10.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.14 40.42 12741 721 99.87 0.18191 0.17852 0.1899 0.23697 0.241 RANDOM 35.809
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] -2.1 -1.05 -2.1 6.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.593 r_dihedral_angle_2_deg 12.056 r_long_range_B_refined 9.005 r_long_range_B_other 9.001 r_dihedral_angle_1_deg 7.412 r_scangle_other 6.487 r_mcangle_it 4.677 r_mcangle_other 4.677 r_scbond_it 4.331 r_scbond_other 4.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.593 r_dihedral_angle_2_deg 12.056 r_long_range_B_refined 9.005 r_long_range_B_other 9.001 r_dihedral_angle_1_deg 7.412 r_scangle_other 6.487 r_mcangle_it 4.677 r_mcangle_other 4.677 r_scbond_it 4.331 r_scbond_other 4.204 r_mcbond_it 3.08 r_mcbond_other 3.079 r_angle_refined_deg 1.618 r_angle_other_deg 0.546 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2183 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing