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Crystal structure of WD40 protein Ciao1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HES PDB entry 2HES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 297 25% PEG 3350, 0.1M (NH4)2SO4, 0.1M Bis-tris, pH6.0, 8% 2,2,2-trifluro ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 1.92 35.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.682 α = 90 b = 74.64 β = 105.05 c = 49.481 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 ADSC QUANTUM 315 2008-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 50 95.7 0.06 0.06 12.5 5.5 30710 30710 17.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 66.5 0.421 0.421 2.62 3.4 1055
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2HES 1.7 47.78 29897 29897 791 95.57 0.16139 0.16139 0.16046 0.19589 0.1916 RANDOM 18.727
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] -0.36 0.22 0.23 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.256 r_dihedral_angle_4_deg 12.926 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_1_deg 6.344 r_scangle_it 2.825 r_scbond_it 1.845 r_angle_refined_deg 1.232 r_mcangle_it 1.229 r_mcbond_it 0.763 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.256 r_dihedral_angle_4_deg 12.926 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_1_deg 6.344 r_scangle_it 2.825 r_scbond_it 1.845 r_angle_refined_deg 1.232 r_mcangle_it 1.229 r_mcbond_it 0.763 r_nbtor_refined 0.298 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_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 2538 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 5
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling