3A9B

CcCel6C, a glycoside hydrolase family 6 enzyme, complexed with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A64PDB ENTRY 3A64

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729330% PEG 8000, 0.1M HEPES-KOH, 0.15M magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.168α = 77.57
b = 45.395β = 86.91
c = 49.128γ = 68.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.223.5892.90.03629.42100613
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)
1.21.2489.40.1843.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3A641.223.5895592501792.620.148610.147530.16892RANDOM15.124
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]
0.03-0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.792
r_dihedral_angle_4_deg17.47
r_dihedral_angle_3_deg11.215
r_dihedral_angle_1_deg5.624
r_sphericity_bonded3.62
r_sphericity_free3.516
r_scangle_it2.751
r_scbond_it2.433
r_rigid_bond_restr2.17
r_mcangle_it1.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.792
r_dihedral_angle_4_deg17.47
r_dihedral_angle_3_deg11.215
r_dihedral_angle_1_deg5.624
r_sphericity_bonded3.62
r_sphericity_free3.516
r_scangle_it2.751
r_scbond_it2.433
r_rigid_bond_restr2.17
r_mcangle_it1.297
r_angle_refined_deg1.202
r_mcbond_it0.858
r_nbtor_refined0.315
r_symmetry_vdw_refined0.218
r_nbd_refined0.203
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.094
r_chiral_restr0.084
r_symmetry_metal_ion_refined0.024
r_metal_ion_refined0.018
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2959
Nucleic Acid Atoms
Solvent Atoms579
Heterogen Atoms37

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling