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Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 15% PEG3350, 0.1 M HEPES pH 7.5, 0.2M NaCl, 277 K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.94 75.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.396 α = 90 b = 149.396 β = 90 c = 62.175 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.97622 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 129.38 99.6 0.07 0.072 0.017 13.8 17.8 24683
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 2.69 96.1 0.687 0.716 0.192 0.908 12
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 4BIS 2.6 30 21751 1112 92.39 0.1706 0.1681 0.1743 0.222 0.2291 RANDOM 43.64
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_dihedral_angle_4_deg 23.161 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_1_deg 7.222 r_angle_refined_deg 1.959 r_angle_other_deg 0.948 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_dihedral_angle_4_deg 23.161 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_1_deg 7.222 r_angle_refined_deg 1.959 r_angle_other_deg 0.948 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2799 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction