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Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-beta-D-ManNAcOMe
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 289 0.1 M Bis-Tris, pH 6.5, 28% PEG2000 MME
Crystal Properties Matthews coefficient Solvent content 2.13 36.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.543 α = 90 b = 65.834 β = 90 c = 71.919 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 289 CCD MARMOSAIC 300 mm CCD 2016-06-27 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 1.24 30 99.2 0.04 0.045 0.02 16.1 4.1 44339
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 1.24 1.28 97.3 0.693 0.844 0.473 0.66 2.8 3548
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 1.24 30 42050 2218 98.91 0.1483 0.1466 0.1484 0.1789 0.1807 RANDOM 18.404
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] 1.25 0.01 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.592 r_sphericity_free 20.465 r_dihedral_angle_4_deg 13.383 r_dihedral_angle_3_deg 12.183 r_sphericity_bonded 8.726 r_dihedral_angle_1_deg 5.084 r_rigid_bond_restr 1.787 r_mcangle_it 1.726 r_angle_refined_deg 1.481 r_mcbond_it 1.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.592 r_sphericity_free 20.465 r_dihedral_angle_4_deg 13.383 r_dihedral_angle_3_deg 12.183 r_sphericity_bonded 8.726 r_dihedral_angle_1_deg 5.084 r_rigid_bond_restr 1.787 r_mcangle_it 1.726 r_angle_refined_deg 1.481 r_mcbond_it 1.381 r_mcbond_other 1.376 r_angle_other_deg 0.932 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1276 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing