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Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GP5
Crystallization Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.294 α = 90 b = 148.964 β = 90 c = 56.81 γ = 90
Symmetry Space Group P 21 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 200 CCD MARMOSAIC 300 mm CCD 2007-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.000 APS 23-ID-D
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 2.05 37.6 0.056 11.4 5.8 54092 2 1
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) 2.05 2.12 0.463 3.1 6 5343
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2gp5 2.05 29.97 1 2 54030 2753 99.57 0.21501 0.21261 0.2536 0.25966 0.2803 RANDOM 47.433
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 18.279 r_dihedral_angle_3_deg 16.516 r_dihedral_angle_1_deg 6.446 r_scangle_it 3.139 r_scbond_it 2.201 r_angle_refined_deg 1.561 r_mcangle_it 1.362 r_mcbond_it 0.86 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 18.279 r_dihedral_angle_3_deg 16.516 r_dihedral_angle_1_deg 6.446 r_scangle_it 3.139 r_scbond_it 2.201 r_angle_refined_deg 1.561 r_mcangle_it 1.362 r_mcbond_it 0.86 r_nbtor_refined 0.311 r_metal_ion_refined 0.258 r_xyhbond_nbd_refined 0.239 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.201 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5614 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection d*TREK data reduction d*TREK data scaling MOLREP phasing