4D5I | pdb_00004d5i

Hypocrea jecorina cellobiohydrolase Cel7A E212Q 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 DROP62980.1 M NA-MES (PH 6.0), 20% MONOMETHYL ETHER PEG 5000, 0.01 M COCL2, 12.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.0838.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.447α = 90
b = 83.094β = 90
c = 110.579γ = 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
11.4229.4497.40.0424.36.9700072
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)
11.421.5910.2685.2

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 3CEL1.4266.6166258352496.910.19840.19670.20.230170.24RANDOM16.158
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]
-1.512.12-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.12
r_dihedral_angle_4_deg17.372
r_dihedral_angle_3_deg11.526
r_dihedral_angle_1_deg6.246
r_angle_refined_deg1.327
r_mcangle_it1.186
r_scbond_it1.028
r_mcbond_it0.74
r_chiral_restr0.09
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.12
r_dihedral_angle_4_deg17.372
r_dihedral_angle_3_deg11.526
r_dihedral_angle_1_deg6.246
r_angle_refined_deg1.327
r_mcangle_it1.186
r_scbond_it1.028
r_mcbond_it0.74
r_chiral_restr0.09
r_bond_refined_d0.009
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 Atoms609
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing