☰ Navigation Tabs
Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Drops consisting of 400 nL of mother-liquor and protein solution (AaSiaP at 20 mg/mL along with and without 0.75 mM Neu5Ac in SEC buffer) were mixed using the Mosquito Protein Crystallization System and the sitting-drop vapor-diffusion method and incubated at 20 C. Neu5Ac (0.75 mM) bound AaSiaP crystals including grew in SG1 condition H2 (30% w/v PEG 4000) were not cryo-protected before being flash-cooled in liquid nitrogen prior to data collection
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.166 α = 90 b = 49.54 β = 92.81 c = 121.389 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 110 PIXEL DECTRIS EIGER X 16M 2019-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.91840 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.9 45.86 99.76 0.995 6.2 2 62386 25.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 0.505
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 45.81 1.35 62368 3107 99.95 0.2015 0.1999 0.2001 0.2317 0.2318 30.42
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 6.9058 f_angle_d 1.4157 f_chiral_restr 0.0748 f_bond_d 0.0143 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4818 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing