2PB1

Exo-B-(1,3)-Glucanase from Candida Albicans in complex with unhydrolysed and covalently linked 2,4-dinitrophenyl-2-deoxy-2-fluoro-B-D-glucopyranoside at 1.9 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EQPPDB entry 1EQP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.3293PEG 8000, Hepes, CaCl2, pH 7.3, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.0941.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.149α = 90
b = 65.586β = 90
c = 96.966γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS II1997-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.92091.60.04714.83089828359
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)
11.91.9791.40.2092779

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1EQP1.919.9228340118291.720.1350.1330.162RANDOM20.534
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.616
r_dihedral_angle_4_deg16.96
r_dihedral_angle_3_deg12.747
r_dihedral_angle_1_deg5.84
r_scangle_it3.307
r_scbond_it2.335
r_mcangle_it1.452
r_angle_refined_deg1.334
r_mcbond_it1.042
r_angle_other_deg0.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.616
r_dihedral_angle_4_deg16.96
r_dihedral_angle_3_deg12.747
r_dihedral_angle_1_deg5.84
r_scangle_it3.307
r_scbond_it2.335
r_mcangle_it1.452
r_angle_refined_deg1.334
r_mcbond_it1.042
r_angle_other_deg0.975
r_mcbond_other0.237
r_symmetry_vdw_other0.228
r_nbd_refined0.211
r_symmetry_hbond_refined0.201
r_xyhbond_nbd_refined0.198
r_nbd_other0.197
r_nbtor_refined0.187
r_symmetry_vdw_refined0.143
r_nbtor_other0.09
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3214
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing