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The Crystal Structure of JMJD2A(M1-L359) from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M KSCN, 0.1M Bis-Tris propane pH7.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.641 α = 90 b = 97.111 β = 90 c = 141.083 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 EIGER X 9M 2020-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18057 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.3 48.603 99.8 0.162 0.996 6.9 5.6 11222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.56 0.675 0.867
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 3.3 48.603 11190 560 99.608 0.246 0.2439 0.2461 0.2928 0.2921 96.393
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] 10.332 -6.986 -3.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.962 r_dihedral_angle_6_deg 12.679 r_lrange_it 11.771 r_lrange_other 11.771 r_mcangle_it 6.518 r_mcangle_other 6.518 r_dihedral_angle_1_deg 6.384 r_scangle_it 5.898 r_scangle_other 5.898 r_mcbond_it 3.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.962 r_dihedral_angle_6_deg 12.679 r_lrange_it 11.771 r_lrange_other 11.771 r_mcangle_it 6.518 r_mcangle_other 6.518 r_dihedral_angle_1_deg 6.384 r_scangle_it 5.898 r_scangle_other 5.898 r_mcbond_it 3.95 r_mcbond_other 3.949 r_dihedral_angle_2_deg 3.843 r_scbond_it 3.726 r_scbond_other 3.725 r_angle_refined_deg 1.025 r_angle_other_deg 0.336 r_symmetry_nbd_refined 0.314 r_nbd_other 0.249 r_nbd_refined 0.219 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.057 r_symmetry_xyhbond_nbd_refined 0.05 r_chiral_restr 0.044 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 5482 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing