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Crystal structure of Wild type Vps29 from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 200 mM Sodium Acetate, 100mM Sodium cacodylate pH 6.5, 30% PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.18 43.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.564 α = 90 b = 78.771 β = 90.1 c = 67.974 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 MAR CCD 165 mm 2016-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.86 50 99.9 39 7.6 31246
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 1w24 1.86 31.534 1.34 31246 1571 99.18 0.2004 0.1979 0.1989 0.2471 0.2477
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 15.376 f_angle_d 1.047 f_chiral_restr 0.066 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2787 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data processing SCALEPACK data scaling PHASER phasing PHENIX refinement