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Crystal structure of the oligomeric rMcL-1 in complex with raffinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 18% PEG 4000, 50 mM sodium acetate, 0.1 M HEPES, 0.1 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.52 α = 90 b = 77.934 β = 89.89 c = 156.285 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 101 PIXEL DECTRIS PILATUS 200K 2017-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.09 49.34 99.6 0.136 0.148 0.048 0.804 29.2 7.8 159786 36.97
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 2.09 2.11 97.5 0.704 2.3 5.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.09 49.34 1.34 159786 3796 89.54 0.2168 0.2016 0.2359 0.221 39.46
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 14.1786 f_angle_d 1.0321 f_chiral_restr 0.0599 f_plane_restr 0.0061 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9599 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 942
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing