4D5J | pdb_00004d5j

Hypocrea jecorina cellobiohydrolase Cel7A E217Q soaked with xylotriose.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CELPDB ENTRY 3CEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP60.1 M MES (PH 6.0), 20% MONOMETHYL ETHER PEG 5000, 0.01 M COCL2, 12.5% GLYCEROL, VAPOR DIFFUSION - HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.0840.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.232α = 90
b = 83.083β = 90
c = 110.66γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MAR165MIRRORS2011-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
11.4229.498.80.053414708922
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)
11.421.594.30.2810.910.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3CEL1.566.5258041309999.260.172540.171130.170.198970.2RANDOM14.729
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]
-0.981.6-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.786
r_dihedral_angle_4_deg17.531
r_dihedral_angle_3_deg11.566
r_dihedral_angle_1_deg6.09
r_angle_refined_deg1.287
r_mcangle_it1.099
r_scbond_it0.834
r_mcbond_it0.66
r_chiral_restr0.086
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.786
r_dihedral_angle_4_deg17.531
r_dihedral_angle_3_deg11.566
r_dihedral_angle_1_deg6.09
r_angle_refined_deg1.287
r_mcangle_it1.099
r_scbond_it0.834
r_mcbond_it0.66
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.007
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_other
r_mcangle_other
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 Atoms593
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing