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Crystal structure of PHF13 in complex with H3K4me3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O70 PDB ENTRY 3O70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1M Tris-HCl pH 8.5;
1.5M Na-Citrate,
PEG400 6%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.09 36.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.232 α = 90 b = 44.334 β = 90 c = 60.33 γ = 90
Symmetry Space Group P 21 21 21
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 315 2010-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97941 APS 19-ID
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 1.66 50 0.032 7.4 7142 6772
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 (All) 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 PDB ENTRY 3O70 1.67 35.73 6772 334 99.85 0.1851 0.1851 0.1832 0.1862 0.2243 0.2272 RANDOM 20.8941
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] -0.12 0.11 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_4_deg 18.409 r_dihedral_angle_3_deg 16.099 r_scangle_it 6.361 r_dihedral_angle_1_deg 5.6 r_scbond_it 3.704 r_mcangle_it 2.757 r_mcbond_it 1.696 r_angle_refined_deg 1.586 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_4_deg 18.409 r_dihedral_angle_3_deg 16.099 r_scangle_it 6.361 r_dihedral_angle_1_deg 5.6 r_scbond_it 3.704 r_mcangle_it 2.757 r_mcbond_it 1.696 r_angle_refined_deg 1.586 r_chiral_restr 0.141 r_bond_refined_d 0.02 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 467 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing