☰ Navigation Tabs
Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.1M bis-tris pH 5.5, 24% PEG3350, 0.4M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.6 α = 90 b = 93.79 β = 107.5 c = 92.61 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2015-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9282 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.07 54.934 99.2 0.085 0.13 0.069 0.996 10.2 3.4 56778 32.041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 9.26 99.1 0.961 0.713 0.556 1.3 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6RBJ 2.07 54.934 56756 2774 99.122 0.172 0.1696 0.1704 0.2137 0.2151 40.58
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] 3.129 0.238 -3.372 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.67 r_dihedral_angle_4_deg 15.386 r_dihedral_angle_3_deg 14.616 r_dihedral_angle_1_deg 7.205 r_lrange_it 3.484 r_lrange_other 3.169 r_scangle_it 2.572 r_scangle_other 2.571 r_mcangle_it 2.465 r_mcangle_other 2.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.67 r_dihedral_angle_4_deg 15.386 r_dihedral_angle_3_deg 14.616 r_dihedral_angle_1_deg 7.205 r_lrange_it 3.484 r_lrange_other 3.169 r_scangle_it 2.572 r_scangle_other 2.571 r_mcangle_it 2.465 r_mcangle_other 2.465 r_scbond_it 2.281 r_scbond_other 2.28 r_mcbond_it 2.147 r_mcbond_other 2.137 r_angle_refined_deg 1.309 r_angle_other_deg 1.233 r_rigid_bond_restr 0.688 r_symmetry_xyhbond_nbd_refined 0.482 r_nbd_other 0.192 r_nbd_refined 0.183 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.059 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5506 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing