1Z3W

Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobioimidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GPIPDB entry 1GPI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7294TRIS-HCl, calcium chloride, PEG 5000, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.382α = 90
b = 46.578β = 102.58
c = 98.505γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal mirror2001-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.9330ESRFID14-2

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
11.74393.20.052142.33978539785
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)
11.71.7992.40.1943.82685

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1GPI1.736.27373343733423501000.181080.178240.22729RANDOM17.761
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]
1.27-0.61-0.25-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.896
r_dihedral_angle_1_deg6.044
r_scangle_it5.472
r_mcangle_it4.842
r_scbond_it4.323
r_mcbond_it4.126
r_angle_refined_deg1.215
r_nbd_refined0.221
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.896
r_dihedral_angle_1_deg6.044
r_scangle_it5.472
r_mcangle_it4.842
r_scbond_it4.323
r_mcbond_it4.126
r_angle_refined_deg1.215
r_nbd_refined0.221
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.138
r_chiral_restr0.086
r_symmetry_hbond_refined0.049
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3198
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing