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Jumonji domain-containing protein 1C with crystallization epitope mutations L2440Y:G2444H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 LFS well F04
20% PEG3350
10% ethylene glycol
0.1M bis-tris-propane pH 6.5
0.2M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.2 α = 90 b = 98.25 β = 92.04 c = 87.4 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 2015-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.98 Diamond I04-1
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 1.78 31.37 98.1 0.086 12 3.4 71577
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 1.78 1.83 99.4 0.936 1.7
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 1.78 31.369 71552 3511 97.995 0.211 0.2093 0.2104 0.2422 0.2413 33.142
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] -1.142 -0.721 1.198 -0.005
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.452 r_dihedral_angle_6_deg 15.601 r_dihedral_angle_3_deg 15.071 r_dihedral_angle_1_deg 7.4 r_dihedral_angle_2_deg 7.147 r_scangle_it 6.711 r_mcangle_it 4.922 r_scbond_it 4.372 r_mcbond_it 3.299 r_angle_refined_deg 1.859
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.452 r_dihedral_angle_6_deg 15.601 r_dihedral_angle_3_deg 15.071 r_dihedral_angle_1_deg 7.4 r_dihedral_angle_2_deg 7.147 r_scangle_it 6.711 r_mcangle_it 4.922 r_scbond_it 4.372 r_mcbond_it 3.299 r_angle_refined_deg 1.859 r_symmetry_nbd_refined 0.491 r_nbd_refined 0.412 r_symmetry_xyhbond_nbd_refined 0.357 r_nbtor_refined 0.314 r_xyhbond_nbd_refined 0.28 r_chiral_restr 0.14 r_ncsr_local_group_1 0.115 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5267 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing