2XSP | pdb_00002xsp

Structure of Cellobiohydrolase 1 (Cel7A) from Heterobasidion annosum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z3VPDB ENTRY 1Z3V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.7PROTEIN WAS CRYSTALLIZED FROM 20 MM MGCL2, 0.1 M HEPES PH 7.7, 20% POLYETHYLENE GLYCOL 3350, THEN SOAKED IN1 MM THIO-XYLOPENTAOSIDE LIGAND SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.1943.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.797α = 90
b = 49.512β = 118.9
c = 73.5γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2010-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-5MAX III911-5

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
11.629.597.30.088.666.47455251.7
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)
11.71.7996.10.332.256.5

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 1Z3V1.728.9743235228997.010.15130.149920.150.177290.18RANDOM15.688
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]
0.19-0.10.48-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.15
r_dihedral_angle_4_deg19.051
r_dihedral_angle_3_deg11.399
r_dihedral_angle_1_deg6.218
r_scangle_it3.588
r_scbond_it2.239
r_angle_refined_deg1.42
r_mcangle_it1.407
r_mcbond_it0.771
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.15
r_dihedral_angle_4_deg19.051
r_dihedral_angle_3_deg11.399
r_dihedral_angle_1_deg6.218
r_scangle_it3.588
r_scbond_it2.239
r_angle_refined_deg1.42
r_mcangle_it1.407
r_mcbond_it0.771
r_chiral_restr0.1
r_bond_refined_d0.012
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_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 Atoms3285
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4Iphasing