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Crystal structure of Drosophila Pygo PHD finger in complex with Legless HD1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VP7 PDB ENTRY 2VP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.136 M (NH4)2SO4, 100 MM TRIS PH 8.3, 200 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.21 α = 90 b = 111.96 β = 90 c = 190.76 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 CCD 2007-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.68 46.18 99.7 0.14 8.7 5 63722 2
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 2.68 2.82 100 0.61 2.2 5.1
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 2VP7 2.68 46.24 60454 3222 99.5 0.22582 0.22389 0.233 0.26231 0.2706 RANDOM 40.824
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] 0.46 -1.54 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.915 r_dihedral_angle_3_deg 19.418 r_dihedral_angle_4_deg 18.922 r_dihedral_angle_1_deg 6.112 r_angle_other_deg 1.859 r_angle_refined_deg 1.597 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_bond_other_d 0.009 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.915 r_dihedral_angle_3_deg 19.418 r_dihedral_angle_4_deg 18.922 r_dihedral_angle_1_deg 6.112 r_angle_other_deg 1.859 r_angle_refined_deg 1.597 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_bond_other_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13607 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing