1Z3T

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


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
2.242.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.414α = 90
b = 46.842β = 102.99
c = 99.488γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41999-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9370ESRFID14-4

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
11.75099.60.098114.34332843328
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)
11.71.7393.10.3215.82867

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1GPI1.740407824078225411000.1720.161250.158790.19866RANDOM20.816
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]
2.53-0.74-1.17-1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.152
r_sphericity_free6.634
r_scangle_it6.12
r_dihedral_angle_1_deg5.299
r_sphericity_bonded4.677
r_scbond_it4.357
r_mcangle_it3.204
r_rigid_bond_restr2.599
r_mcbond_it2.125
r_angle_refined_deg2.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.152
r_sphericity_free6.634
r_scangle_it6.12
r_dihedral_angle_1_deg5.299
r_sphericity_bonded4.677
r_scbond_it4.357
r_mcangle_it3.204
r_rigid_bond_restr2.599
r_mcbond_it2.125
r_angle_refined_deg2.062
r_angle_other_deg0.983
r_nbtor_other0.694
r_symmetry_hbond_refined0.606
r_xyhbond_nbd_refined0.362
r_symmetry_vdw_refined0.357
r_nbd_refined0.35
r_symmetry_vdw_other0.301
r_nbd_other0.211
r_chiral_restr0.135
r_xyhbond_nbd_other0.053
r_bond_refined_d0.026
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3198
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing