2CBJ

Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase in complex with PUGNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CBIPDB ENTRY 2CBI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % PEG 8000) AND 0.25 MICROLITERS OF 40 % V/V GAMMA-BUTYROLACTONE ADDED TO A 1 PLUS 1 MICROLITER DROP
Crystal Properties
Matthews coefficientSolvent content
2.6953.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.613α = 90
b = 145.745β = 90
c = 152.8γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray157IMAGE PLATERIGAKU RAXIS IVMIRRORS2005-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.352093.70.0815.83.9564622
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)
12.352.43960.612.63.6

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 2CBI2.35205583756293.50.1940.1930.248RANDOM42.28
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]
0.891.21-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.814
r_dihedral_angle_4_deg19.39
r_dihedral_angle_3_deg17.001
r_dihedral_angle_1_deg6.514
r_scangle_it5.902
r_scbond_it4.135
r_mcangle_it2.324
r_mcbond_it1.51
r_angle_refined_deg1.366
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.814
r_dihedral_angle_4_deg19.39
r_dihedral_angle_3_deg17.001
r_dihedral_angle_1_deg6.514
r_scangle_it5.902
r_scbond_it4.135
r_mcangle_it2.324
r_mcbond_it1.51
r_angle_refined_deg1.366
r_nbtor_refined0.301
r_symmetry_vdw_refined0.227
r_nbd_refined0.208
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.152
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms9257
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing