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Crystal structure of the catalytic core domain of JMJD2D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other jmjd2a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 hepes, 2.0M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.63 α = 90 b = 71.63 β = 90 c = 151.295 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 130 2007-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 40 36000 34305
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT jmjd2a 1.8 41.24 32633 1693 91.86 0.17554 0.17407 0.2031 RANDOM 21.515
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.478 r_dihedral_angle_4_deg 22.027 r_dihedral_angle_3_deg 15.647 r_dihedral_angle_1_deg 5.933 r_scangle_it 4.884 r_scbond_it 3.51 r_mcangle_it 1.978 r_angle_refined_deg 1.493 r_mcbond_it 1.393 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.478 r_dihedral_angle_4_deg 22.027 r_dihedral_angle_3_deg 15.647 r_dihedral_angle_1_deg 5.933 r_scangle_it 4.884 r_scbond_it 3.51 r_mcangle_it 1.978 r_angle_refined_deg 1.493 r_mcbond_it 1.393 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.282 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.192 r_symmetry_vdw_refined 0.18 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2695 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling