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Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YPD PDB ENTRY 2YPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M BIS-TRIS PH 5.5, 0.1M AMMONIUM ACETATE, 27% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.34 α = 90 b = 85.61 β = 90 c = 117.13 γ = 90
Symmetry Space Group I 2 2 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 PILATUS 6M 2013-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.18 69.12 99.9 0.05 12.2 4.3 22231 2.8
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 2.18 2.25 99.7 0.38 2.8 3.5
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YPD 2.18 69.12 20691 1110 97.96 0.19651 0.1943 0.23911 0.2574 RANDOM 61.731
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] -3.26 -5.38 8.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_4_deg 11.543 r_dihedral_angle_1_deg 5.96 r_mcangle_it 5.426 r_scbond_it 4.75 r_mcbond_it 4.025 r_mcbond_other 3.998 r_angle_refined_deg 1.165 r_angle_other_deg 0.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_4_deg 11.543 r_dihedral_angle_1_deg 5.96 r_mcangle_it 5.426 r_scbond_it 4.75 r_mcbond_it 4.025 r_mcbond_other 3.998 r_angle_refined_deg 1.165 r_angle_other_deg 0.745 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing