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Crystal structure of YadV chaperone at 1.63 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ME0 3ME0, 1KLF, 3F65 experimental model PDB 1KLF 3ME0, 1KLF, 3F65 experimental model PDB 3F65 3ME0, 1KLF, 3F65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 0.1 M ammonium sulfate, 0.1 M sodium acetate, 0.3 M sodium formate, 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.28 α = 90 b = 127.56 β = 90 c = 45.84 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.63 78.838 99.5 0.06 0.064 0.017 21.6 13.1 36961 36961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.72 98.7 0.511 0.511 0.552 0.154 1.4 12.2 5258
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ME0, 1KLF, 3F65 1.63 22.009 1.34 36961 1834 99.52 0.1686 0.1677 0.1729 0.1863 0.1901 35.6368
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 f_dihedral_angle_d 12.584 f_angle_d 1.59 f_chiral_restr 0.087 f_bond_d 0.016 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1550 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement MOSFLM data collection SCALA data scaling PHASER phasing PDB_EXTRACT data extraction iMOSFLM data processing