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Crystal structure of JADE3 PZP domain in complex with Histone H3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GE0 PZP domain of JADE-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M HEPES pH 8.5 and 25% PEG 5000
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.887 α = 90 b = 98.415 β = 90 c = 104.426 γ = 90
Symmetry Space Group P 2 21 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 PILATUS 200K 2025-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 46.12 99.8 0.373 0.152 0.957 5.7 5.9 11979
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 2.6 2.72 99.8 1.046 1.156 0.484 0.6 5.6
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 2.6 29.59 11264 612 99.13 0.23422 0.23189 0.2389 0.27762 0.2746 RANDOM 25.154
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] -2.04 1.85 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.234 r_dihedral_angle_2_deg 13.985 r_dihedral_angle_1_deg 7.618 r_long_range_B_refined 6.466 r_long_range_B_other 6.452 r_mcangle_it 4.28 r_mcangle_other 4.279 r_scangle_other 4.265 r_scbond_it 2.638 r_scbond_other 2.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.234 r_dihedral_angle_2_deg 13.985 r_dihedral_angle_1_deg 7.618 r_long_range_B_refined 6.466 r_long_range_B_other 6.452 r_mcangle_it 4.28 r_mcangle_other 4.279 r_scangle_other 4.265 r_scbond_it 2.638 r_scbond_other 2.637 r_mcbond_it 2.59 r_mcbond_other 2.59 r_angle_refined_deg 1.795 r_angle_other_deg 0.627 r_chiral_restr 0.083 r_bond_refined_d 0.008 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 2575 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction