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The crystal structure of villin domain 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P8X PDB entry 1P8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 The protein(10mg/ml)was mixed in a 1:1 ratio(v/v)with a reservoir solution containing 15%(w/v)PEG8000, 100mM NaOAc buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277KK
Crystal Properties Matthews coefficient Solvent content 2.63 53.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.82 α = 90 b = 47.82 β = 90 c = 98.173 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 CCD ADSC QUANTUM 315 2008-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
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 30 99.6 0.048 4.8 16865
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 2.07 98.8 0.282 3.5
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 1P8X 2 23.91 16008 807 99.7 0.19961 0.19727 0.1913 0.24622 0.2343 RANDOM 38.799
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.129 r_dihedral_angle_3_deg 16.578 r_dihedral_angle_4_deg 11.688 r_dihedral_angle_1_deg 6.139 r_scangle_it 5.302 r_sphericity_free 4.466 r_scbond_it 3.179 r_mcangle_it 2.807 r_rigid_bond_restr 2.299 r_mcbond_it 1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.129 r_dihedral_angle_3_deg 16.578 r_dihedral_angle_4_deg 11.688 r_dihedral_angle_1_deg 6.139 r_scangle_it 5.302 r_sphericity_free 4.466 r_scbond_it 3.179 r_mcangle_it 2.807 r_rigid_bond_restr 2.299 r_mcbond_it 1.683 r_angle_refined_deg 1.499 r_sphericity_bonded 1.431 r_nbtor_refined 0.318 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.205 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.135 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1750 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction