4C4D

Covalent glycosyl-enzyme intermediate of Hypocrea jecorina Cel7a E217Q mutant trapped using DNP-2-deoxy-2-fluoro-cellotrioside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CELPDB ENTRY 7CEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16PROTEIN FIRST INCUBATED WITH 80 UM 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-CELLOTRIOSIDE (DNP-2F-G3)4 IN 10 MM SODIUM MES, PH 6.0. ALIQUOTS WERE TAKEN AT REGULAR TIME INTERVALS AND CONCENTRATED FOR CRYSTALLISATION IN THE PRESENCE OF 1 MM FRESH DNP-2F-G3 ADDED TO THE CRYSTALLISATION DROPS. CRYSTALLISATION CONDITION: 0.1 M MES (PH 6.0), 20% MONOMETHYL ETHER PEG 5000, 0.01 M COCL2, 12% GLYCEROL.
Crystal Properties
Matthews coefficientSolvent content
1.9637.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.93α = 90
b = 83.29β = 90
c = 110.76γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD1999-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.3266.684175

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 7CEL1.3266.5784175441898.470.167740.166750.18673RANDOM11.508
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]
-0.690.7-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.899
r_dihedral_angle_4_deg16.622
r_dihedral_angle_3_deg11.315
r_dihedral_angle_1_deg6.165
r_angle_refined_deg1.271
r_chiral_restr0.086
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.899
r_dihedral_angle_4_deg16.622
r_dihedral_angle_3_deg11.315
r_dihedral_angle_1_deg6.165
r_angle_refined_deg1.271
r_chiral_restr0.086
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms3224
Nucleic Acid Atoms
Solvent Atoms618
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling