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Jumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium acetate,
25% PEG3350,
0.1M bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.03 α = 90 b = 101.6 β = 99.38 c = 141.43 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 6M 2014-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.21 101.6 97.8 0.993 11.7 3.4 77812
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.27 0.606
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 2.21 82.135 77788 3949 97.613 0.217 0.215 0.215 0.2589 0.259 42.601
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] -0.098 -0.303 -0.862 1.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.3 r_dihedral_angle_6_deg 14.508 r_lrange_it 10.106 r_scangle_it 7.675 r_dihedral_angle_2_deg 7.302 r_dihedral_angle_1_deg 7.015 r_mcangle_it 6.938 r_scbond_it 5.491 r_mcbond_it 4.814 r_angle_refined_deg 1.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.3 r_dihedral_angle_6_deg 14.508 r_lrange_it 10.106 r_scangle_it 7.675 r_dihedral_angle_2_deg 7.302 r_dihedral_angle_1_deg 7.015 r_mcangle_it 6.938 r_scbond_it 5.491 r_mcbond_it 4.814 r_angle_refined_deg 1.757 r_symmetry_nbd_refined 0.352 r_nbtor_refined 0.316 r_symmetry_xyhbond_nbd_refined 0.246 r_metal_ion_refined 0.237 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.205 r_chiral_restr 0.129 r_ncsr_local_group_2 0.083 r_ncsr_local_group_3 0.082 r_ncsr_local_group_5 0.08 r_ncsr_local_group_1 0.075 r_ncsr_local_group_4 0.075 r_ncsr_local_group_6 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11115 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing