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Crystal structure of Pizza6-AYW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.1 M MIB (Mixtures of sodium malonate, imidazole, boric acid in the molar rations 2:3:3 buffer) or MMT (Mixtures of DL-malic acid, MES and Tris base in the molar rations 1:2:2 buffer) pH 5.0, 30% (w/v) PEG1500
Crystal Properties Matthews coefficient Solvent content 1.86 33.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.01 α = 90 b = 70.35 β = 100.6 c = 58.21 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 PIXEL DECTRIS PILATUS 2M 2016-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0000 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.3 26.501 94.7 0.062 0.062 8.2 3.2 86627
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 92.6 0.301 0.301 2.8 3.3
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 3WW9 1.3 26.501 1.34 86544 4205 94.65 0.1571 0.1553 0.1556 0.192 0.1922
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 4.002 f_angle_d 1.484 f_chiral_restr 0.156 f_bond_d 0.016 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3580 Nucleic Acid Atoms Solvent Atoms 663 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing