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Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAcOMe (P1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CWC PDB entry 6CWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 0.2 M sodium malonate, pH 7.0, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.215 α = 86.73 b = 72.239 β = 71.29 c = 72.305 γ = 71.4
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 RAYONIX MX-300 2014-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
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 2 40 95 0.044 0.056 0.035 13.8 2.4 53737
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 2 2.03 79.8 0.35 0.446 0.273 0.934 2.2
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 PDB entry 6CWC 2 40 39929 2238 74.44 0.1881 0.1855 0.1939 0.2348 0.2426 RANDOM 33.738
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] -0.19 0.34 0.15 0.2 0.04 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.626 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_4_deg 13.246 r_dihedral_angle_1_deg 5.498 r_mcangle_it 2.142 r_angle_refined_deg 1.605 r_mcbond_it 1.328 r_mcbond_other 1.327 r_angle_other_deg 1.227 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.626 r_dihedral_angle_3_deg 15.366 r_dihedral_angle_4_deg 13.246 r_dihedral_angle_1_deg 5.498 r_mcangle_it 2.142 r_angle_refined_deg 1.605 r_mcbond_it 1.328 r_mcbond_other 1.327 r_angle_other_deg 1.227 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5075 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 84
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing