5GM9

Crystal structure of a glycoside hydrolase in complex with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OA7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298MgCl2, Tris-Cl, PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.337α = 90
b = 54.315β = 90
c = 84.848γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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
11.362599.90.03527.210.846675
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.4199.70.1040.99610.7

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 REPLACEMENTTHROUGHOUT1OA71.362544309230299.760.14260.14140.1643RANDOM15.275
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]
0.09-0.06-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.768
r_dihedral_angle_4_deg11.651
r_dihedral_angle_3_deg9.97
r_dihedral_angle_1_deg7.303
r_mcangle_it2.098
r_angle_refined_deg1.602
r_mcbond_it1.527
r_mcbond_other1.518
r_angle_other_deg0.843
r_chiral_restr0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.768
r_dihedral_angle_4_deg11.651
r_dihedral_angle_3_deg9.97
r_dihedral_angle_1_deg7.303
r_mcangle_it2.098
r_angle_refined_deg1.602
r_mcbond_it1.527
r_mcbond_other1.518
r_angle_other_deg0.843
r_chiral_restr0.313
r_bond_refined_d0.016
r_gen_planes_refined0.015
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1562
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms46

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing