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Crystal structure of catalytic domain of G9a with MS012
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.846 α = 92.09 b = 67.749 β = 90.05 c = 77.845 γ = 91.8
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.72 50 96.4 0.075 0.09 0.049 9.4 3.1 119007
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 83.5 0.55 0.82 2.5
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 MOLECULAR REPLACEMENT THROUGHOUT 3K5K 1.72 50.01 117616 1275 96.46 0.207 0.2066 0.2125 0.2473 0.2477 RANDOM 28.993
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] -2.34 -1.4 0.33 0.18 -0.35 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.167 r_dihedral_angle_4_deg 15.278 r_dihedral_angle_3_deg 12.204 r_dihedral_angle_1_deg 5.864 r_mcangle_it 2.498 r_mcbond_it 1.622 r_mcbond_other 1.622 r_angle_refined_deg 1.488 r_angle_other_deg 1.04 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.167 r_dihedral_angle_4_deg 15.278 r_dihedral_angle_3_deg 12.204 r_dihedral_angle_1_deg 5.864 r_mcangle_it 2.498 r_mcbond_it 1.622 r_mcbond_other 1.622 r_angle_refined_deg 1.488 r_angle_other_deg 1.04 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8325 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction PHASER phasing HKL-3000 data reduction