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Jumonji domain-containing protein 2B with crown ether and crystallization epitope mutations L916G:R917A:A918D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Hampton Index well B7
0.056 M sodium phosphate monobasic
1.344 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 3.61 65.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.93 α = 90 b = 87.93 β = 90 c = 142.91 γ = 120
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 2016-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.74 32.31 99.3 0.053 20.5 8.7 21921
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 1.74 1.79 0.746
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.74 32.308 21920 1107 99.257 0.204 0.203 0.2029 0.2251 0.2249 39.68
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] 0.007 0.003 0.007 -0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.02 r_lrange_it 13.35 r_dihedral_angle_3_deg 12.026 r_scangle_it 7.609 r_dihedral_angle_2_deg 7.558 r_dihedral_angle_1_deg 6.632 r_scbond_it 5.512 r_mcangle_it 4.94 r_mcbond_it 3.869 r_angle_refined_deg 2.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.02 r_lrange_it 13.35 r_dihedral_angle_3_deg 12.026 r_scangle_it 7.609 r_dihedral_angle_2_deg 7.558 r_dihedral_angle_1_deg 6.632 r_scbond_it 5.512 r_mcangle_it 4.94 r_mcbond_it 3.869 r_angle_refined_deg 2.048 r_symmetry_nbd_refined 0.636 r_symmetry_xyhbond_nbd_refined 0.383 r_nbtor_refined 0.318 r_nbd_refined 0.282 r_xyhbond_nbd_refined 0.227 r_chiral_restr 0.147 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1010 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing