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The Crystal Structure of human JMJD2A Tudor domain from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M NaCl, 0.1M HEPES pH7.5, 1.6M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.42 63.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.11 α = 90 b = 135.11 β = 90 c = 135.11 γ = 90
Symmetry Space Group I 41 3 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 2020-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976253 ESRF ID30B
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 2.2 67.56 99.9 0.129 21.4 41.4 11007
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 2.2 2.26 2.749
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2gf7 2.201 55.219 10991 558 99.918 0.232 0.2297 0.2358 0.2722 0.2781 52.144
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 r_dihedral_angle_2_deg 35.976 r_dihedral_angle_3_deg 14.457 r_dihedral_angle_1_deg 7.569 r_lrange_it 6.89 r_lrange_other 6.872 r_dihedral_angle_4_deg 6.616 r_scangle_it 5.267 r_scangle_other 5.25 r_mcangle_other 3.698 r_mcangle_it 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.976 r_dihedral_angle_3_deg 14.457 r_dihedral_angle_1_deg 7.569 r_lrange_it 6.89 r_lrange_other 6.872 r_dihedral_angle_4_deg 6.616 r_scangle_it 5.267 r_scangle_other 5.25 r_mcangle_other 3.698 r_mcangle_it 3.68 r_scbond_it 3.211 r_scbond_other 3.185 r_mcbond_it 2.435 r_mcbond_other 2.392 r_angle_refined_deg 1.255 r_angle_other_deg 1.197 r_nbd_other 0.19 r_symmetry_nbd_other 0.181 r_nbd_refined 0.177 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.123 r_symmetry_xyhbond_nbd_refined 0.081 r_symmetry_nbtor_other 0.073 r_symmetry_nbd_refined 0.052 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 930 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing