☰ Navigation Tabs
Asymmetric trimer of the Drosophila melanogaster DCP1 C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WX3 PDB ENTRY 2WX3 TRUNCATED POLY-ALA MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100 MM MES (PH6.5), 1.2 M AMMONIUM SULFATE, 5% 1,4-DIOXANE
Crystal Properties Matthews coefficient Solvent content 4.5 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.92 α = 90 b = 120.92 β = 90 c = 134.47 γ = 120
Symmetry Space Group P 61 2 2
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 MARRESEARCH MIRRORS 2009-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 50 98.2 0.11 13 4.8 14564 55.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 96 0.8 2 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WX3 TRUNCATED POLY-ALA MODEL 2.8 48.79 13830 730 98.21 0.21725 0.21482 0.26675 0.2275 RANDOM 43.18
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] 0.16 0.08 0.16 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.958 r_dihedral_angle_3_deg 18.34 r_dihedral_angle_1_deg 5.022 r_scangle_it 3.223 r_scbond_it 1.862 r_mcangle_it 1.531 r_angle_refined_deg 1.272 r_mcbond_it 0.782 r_chiral_restr 0.083 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.958 r_dihedral_angle_3_deg 18.34 r_dihedral_angle_1_deg 5.022 r_scangle_it 3.223 r_scbond_it 1.862 r_mcangle_it 1.531 r_angle_refined_deg 1.272 r_mcbond_it 0.782 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other 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 2053 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing