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Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CEY experimental model PDB 2WYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 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. Apo AaSiaP crystals that grew in SG1 conditions C11 (0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate, pH 6.5, 30% (w/v) PEG 8000)
Crystal Properties Matthews coefficient Solvent content 3.63 66.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.667 α = 90 b = 141.394 β = 112.491 c = 109.405 γ = 90
Symmetry Space Group C 1 2 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 2.58 48.64 100 0.995 6.3 3.6 61226
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 2.58 2.65 0.783 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.58 48.64 58058 3158 99.94 0.19069 0.18906 0.1945 0.21965 0.2184 RANDOM 61.518
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] 0.53 -0.9 1.09 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.228 r_long_range_B_refined 8.714 r_long_range_B_other 8.714 r_scangle_other 7.229 r_dihedral_angle_1_deg 6.093 r_mcangle_other 5.238 r_mcangle_it 5.233 r_scbond_it 4.686 r_scbond_other 4.656 r_mcbond_it 3.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.228 r_long_range_B_refined 8.714 r_long_range_B_other 8.714 r_scangle_other 7.229 r_dihedral_angle_1_deg 6.093 r_mcangle_other 5.238 r_mcangle_it 5.233 r_scbond_it 4.686 r_scbond_other 4.656 r_mcbond_it 3.497 r_mcbond_other 3.484 r_angle_refined_deg 1.53 r_angle_other_deg 0.522 r_chiral_restr 0.072 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9608 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing