X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6MCW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4293PEG 3350, potassium phosphate, (2R,3R,4S,5S,6R)-2-(((2R,3S,4R,5R,6R)-6-(dodecyloxy)-4,5-dihydroxy-2-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)oxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol
Crystal Properties
Matthews coefficientSolvent content
2.957.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.397α = 90
b = 101.561β = 90
c = 122.004γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300BE LENS2022-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.953089.480.0690.0220.9934.19.59120520.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.98280.5330.6321.26.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6mcw1.9528.0877442406289.440.19490.19330.2251RANDOM25.24
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]
-0.020.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.771
r_dihedral_angle_3_deg13.953
r_dihedral_angle_4_deg13.485
r_dihedral_angle_1_deg7.428
r_angle_other_deg1.287
r_angle_refined_deg1.22
r_chiral_restr0.063
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.771
r_dihedral_angle_3_deg13.953
r_dihedral_angle_4_deg13.485
r_dihedral_angle_1_deg7.428
r_angle_other_deg1.287
r_angle_refined_deg1.22
r_chiral_restr0.063
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_refined_d0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7122
Nucleic Acid Atoms
Solvent Atoms784
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing