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Jumonji domain-containing protein 2D with crystallization epitope mutation Q41R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Hampton Index H08
0.1M magnesium formate
15% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.167 α = 90 b = 73.167 β = 90 c = 134.44 γ = 120
Symmetry Space Group P 32 2 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 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98010 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.04 44.81 100 0.061 21.1 9.7 27244
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 2.04 2.09 0.791
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.013 57.32 28289 1387 100 0.2263 0.2251 0.2118 0.2501 0.2268 RANDOM 51.57
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] 1.8101 1.8101 -3.6203
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.89 t_omega_torsion 3.76 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2665 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 2
Software Software Software Name Purpose BUSTER refinement xia2 data reduction xia2 data scaling PHASER phasing