☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS039332c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RBJ 6RBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.1M bis-tris pH 5.5 21% PEG3350 0.3M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.6 α = 90 b = 93.69 β = 108.03 c = 93.434 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.92819 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 1.68 88.85 99 0.044 0.053 0.028 0.999 14.6 3.4 106186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 98.6 1.188 1.415 0.759 0.545 3.3 7816
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 FOURIER SYNTHESIS THROUGHOUT 6RBJ 1.68 88.85 100785 5376 98.87 0.1904 0.1888 0.2213 0.2213 0.2509 RANDOM 35.588
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] 1.64 -0.07 -2.02 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.952 r_dihedral_angle_4_deg 16.936 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_1_deg 7.44 r_mcangle_it 4.797 r_mcbond_other 3.087 r_mcbond_it 3.061 r_angle_refined_deg 1.611 r_angle_other_deg 1.296 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.952 r_dihedral_angle_4_deg 16.936 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_1_deg 7.44 r_mcangle_it 4.797 r_mcbond_other 3.087 r_mcbond_it 3.061 r_angle_refined_deg 1.611 r_angle_other_deg 1.296 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5512 Nucleic Acid Atoms Solvent Atoms 658 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing