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X-ray crystal structure of Y16524 in EP300
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 60% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.369 α = 90 b = 55.983 β = 90 c = 114.135 γ = 90
Symmetry Space Group I 2 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 80 PIXEL DECTRIS PILATUS3 6M 2023-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 1.28 45.47 99.7 0.059 0.062 0.019 0.999 19.9 9.7 38973
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 1.28 1.3 95.5 0.412 0.467 0.214 0.878 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7UGI 2.13 29.92 8518 488 99.91 0.18532 0.18237 0.1916 0.23414 0.2376 RANDOM 23.151
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] -1.67 3.14 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.305 r_dihedral_angle_3_deg 16.888 r_dihedral_angle_4_deg 15.948 r_dihedral_angle_1_deg 6.152 r_long_range_B_refined 6.008 r_long_range_B_other 5.987 r_scangle_other 4.686 r_scbond_it 2.933 r_scbond_other 2.93 r_mcangle_it 2.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.305 r_dihedral_angle_3_deg 16.888 r_dihedral_angle_4_deg 15.948 r_dihedral_angle_1_deg 6.152 r_long_range_B_refined 6.008 r_long_range_B_other 5.987 r_scangle_other 4.686 r_scbond_it 2.933 r_scbond_other 2.93 r_mcangle_it 2.923 r_mcangle_other 2.907 r_mcbond_it 1.962 r_mcbond_other 1.901 r_angle_refined_deg 1.674 r_angle_other_deg 1.566 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 986 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing