1UY3 | pdb_00001uy3

Binding sub-site dissection of a family 6 carbohydrate-binding module by X-ray crystallography and isothermal titration calorimetry


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GMMPDB ENTRY 1GMM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5pH 4.50
Crystal Properties
Matthews coefficientSolvent content
2.5551.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.413α = 90
b = 83.413β = 90
c = 44.659γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU R-AXIS IV++OSMIC BLUEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-002

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.892099.90.07168.212433
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.961000.3545.28

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GMM1.89201243366299.90.1320.130.170.1660.19RANDOM24.18
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]
-0.74-0.741.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.54
r_scangle_it6.126
r_scbond_it4.251
r_mcangle_it2.62
r_mcbond_it1.728
r_angle_refined_deg1.631
r_angle_other_deg0.872
r_symmetry_hbond_refined0.312
r_nbd_other0.265
r_symmetry_vdw_other0.246
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms986
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing