6RYM

Structure of carbohydrate recognition domain with GlcNAc bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82932.5 M ammonium sulfate, 0.1 M tris
Crystal Properties
Matthew coefficientSolvent content
2.3347.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.225α = 90
b = 50.225β = 90
c = 51.925γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.488SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)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
11.45725.10680.80.0360.0360.05431.56.518321
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.5421.80.1210.1210.1862.82.6

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 REPLACEMENTTHROUGHOUTpdbid 6RYJ1.4625.1061735594580.790.16250.16140.1841RANDOM14.2
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]
-0.23-0.230.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.414
r_dihedral_angle_4_deg19.271
r_dihedral_angle_3_deg11.027
r_dihedral_angle_1_deg6.704
r_angle_refined_deg1.38
r_angle_other_deg0.974
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.414
r_dihedral_angle_4_deg19.271
r_dihedral_angle_3_deg11.027
r_dihedral_angle_1_deg6.704
r_angle_refined_deg1.38
r_angle_other_deg0.974
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms940
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms32

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing