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Crystal structure of the thioredoxin-fold domain of human phosducin-like protein 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBC PDB ENTRY 2DBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 28%(w/v) PEG8000, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.594 α = 90 b = 44.594 β = 90 c = 141.971 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH mirrors 2008-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 2.7 26.14 93.9 0.175 10.22 2.7 9164 8421 2 65.5
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 2.69 2.8 88.6 0.614 1.53 2 895
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 2DBC 2.7 18.88 7998 394 96.77 0.23615 0.23411 0.2324 0.27576 0.2725 RANDOM 42.302
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.551 r_dihedral_angle_4_deg 28.456 r_dihedral_angle_3_deg 20.476 r_dihedral_angle_1_deg 5.866 r_scangle_it 1.409 r_angle_refined_deg 1.221 r_scbond_it 0.874 r_mcangle_it 0.622 r_mcbond_it 0.326 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.551 r_dihedral_angle_4_deg 28.456 r_dihedral_angle_3_deg 20.476 r_dihedral_angle_1_deg 5.866 r_scangle_it 1.409 r_angle_refined_deg 1.221 r_scbond_it 0.874 r_mcangle_it 0.622 r_mcbond_it 0.326 r_nbtor_refined 0.307 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 1898 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 16
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling