☰ Navigation Tabs
Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 0.1M HEPES, PH 7.4, 2.2M AMSO4
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.416 α = 90 b = 71.416 β = 90 c = 150.292 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 100 CCD SATURN A200 2010-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 2.03 40 92.5 0.43 16.1 6 25162 2
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 2.03 94 0.43 4.4 5.7
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 NONE 2 64.5 24068 1028 92.45 0.15897 0.15673 0.1686 0.21141 0.2226 RANDOM 21.925
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] 0.41 0.41 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_4_deg 18.689 r_dihedral_angle_3_deg 12.027 r_dihedral_angle_1_deg 5.481 r_mcangle_it 1.629 r_scbond_it 1.377 r_angle_refined_deg 1.035 r_mcbond_it 0.967 r_mcbond_other 0.963 r_angle_other_deg 0.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_4_deg 18.689 r_dihedral_angle_3_deg 12.027 r_dihedral_angle_1_deg 5.481 r_mcangle_it 1.629 r_scbond_it 1.377 r_angle_refined_deg 1.035 r_mcbond_it 0.967 r_mcbond_other 0.963 r_angle_other_deg 0.717 r_chiral_restr 0.065 r_bond_refined_d 0.005 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 2657 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling