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The Crystal Structure of JMJD2D from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M HEPES, NaOH pH 7.5, 2% PEG 400, 2M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.34 α = 90 b = 71.34 β = 90 c = 150.873 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2023-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978530 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 47.89 92 0.029 60.6 15.9 40301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 0.162 13.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 47.887 40220 2006 92.009 0.163 0.1612 0.1735 0.1876 0.1981 19.554
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] 0.597 0.597 -1.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.821 r_dihedral_angle_3_deg 12.19 r_dihedral_angle_1_deg 6.476 r_dihedral_angle_2_deg 6.231 r_lrange_it 5.695 r_lrange_other 5.38 r_scangle_it 2.958 r_scangle_other 2.958 r_mcangle_it 1.896 r_mcangle_other 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.821 r_dihedral_angle_3_deg 12.19 r_dihedral_angle_1_deg 6.476 r_dihedral_angle_2_deg 6.231 r_lrange_it 5.695 r_lrange_other 5.38 r_scangle_it 2.958 r_scangle_other 2.958 r_mcangle_it 1.896 r_mcangle_other 1.896 r_scbond_it 1.889 r_scbond_other 1.888 r_mcbond_it 1.184 r_mcbond_other 1.184 r_angle_refined_deg 1.131 r_angle_other_deg 0.399 r_nbd_refined 0.211 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.169 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.117 r_nbd_other 0.107 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.059 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2687 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing