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Crystal structure of WDR5 mutant (W330Y)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H14 PDB ENTRY 2H14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 18% PEG 3350, 0.1M Hepes, 14mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.748 α = 90 b = 79.68 β = 101.91 c = 45.79 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 CCD RIGAKU SATURN 944+ confocal 2010-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002+ 1.5418
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 2.5 39.05 100 0.113 10.6 6.81 10708
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) 2.5 2.59 100 0.158 7.1 6.82
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 PDB ENTRY 2H14 2.5 39.05 10707 504 99.93 0.22243 0.21741 0.2195 0.32332 0.3211 RANDOM 11.942
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] 0.17 0.11 -0.09 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.801 r_dihedral_angle_4_deg 20.293 r_dihedral_angle_3_deg 17.976 r_dihedral_angle_1_deg 7.705 r_scangle_it 2.487 r_scbond_it 1.571 r_angle_refined_deg 1.526 r_mcangle_it 1.017 r_mcbond_it 0.554 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.801 r_dihedral_angle_4_deg 20.293 r_dihedral_angle_3_deg 17.976 r_dihedral_angle_1_deg 7.705 r_scangle_it 2.487 r_scbond_it 1.571 r_angle_refined_deg 1.526 r_mcangle_it 1.017 r_mcbond_it 0.554 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2434 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement d*TREK data reduction d*TREK data scaling