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Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAcOMe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.303 α = 90 b = 65.611 β = 90 c = 72.29 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 200K 2019-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 20 98.2 0.099 0.113 0.053 8.1 4.3 13823
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 99.3 0.54 0.646 0.345 0.795 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6CWM 1.85 19.63 13083 694 97.74 0.1877 0.1861 0.1952 0.2173 0.2295 RANDOM 21.533
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] 2.21 -0.86 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.091 r_dihedral_angle_4_deg 11.914 r_dihedral_angle_3_deg 11.875 r_dihedral_angle_1_deg 5.617 r_angle_other_deg 1.27 r_angle_refined_deg 1.228 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.091 r_dihedral_angle_4_deg 11.914 r_dihedral_angle_3_deg 11.875 r_dihedral_angle_1_deg 5.617 r_angle_other_deg 1.27 r_angle_refined_deg 1.228 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1268 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing