1UY3

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GMM1.89201243366299.90.1320.130.166RANDOM24.18
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
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
r_nbd_refined0.208
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.174
r_metal_ion_refined0.131
r_chiral_restr0.109
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
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