1Z3V

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


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
2.142.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.947α = 90
b = 46.7β = 102.77
c = 99.124γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41999-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9322ESRFID14-4

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
11.65099.30.07214.83.45027250272
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)
11.61.6399.60.2388.13286

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 1GPI1.6139.22472744727429981000.16050.157880.20197RANDOM22.962
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]
1.47-0.94-0.34-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.097
r_sphericity_free10.552
r_sphericity_bonded8.045
r_dihedral_angle_1_deg6.681
r_scangle_it5.972
r_scbond_it4.634
r_mcangle_it3.573
r_rigid_bond_restr2.859
r_mcbond_it2.68
r_angle_refined_deg1.511
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.097
r_sphericity_free10.552
r_sphericity_bonded8.045
r_dihedral_angle_1_deg6.681
r_scangle_it5.972
r_scbond_it4.634
r_mcangle_it3.573
r_rigid_bond_restr2.859
r_mcbond_it2.68
r_angle_refined_deg1.511
r_symmetry_hbond_refined0.788
r_symmetry_vdw_refined0.339
r_nbd_refined0.233
r_xyhbond_nbd_refined0.162
r_chiral_restr0.14
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3198
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing