2EPN

N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EPKPDB entry 2EPK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100mM HEPES, 2M ammonium sulphate, 0.5%(v/v) PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.574α = 90
b = 112.332β = 90
c = 103.127γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirror2006-11-28MSINGLE 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
11.6115.0299.340.06420.99.11621031610333318.2
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)
11.611.6594.370.53.518.4

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 2EPK1.6115.02162103161033802899.340.169120.169120.16740.20186RANDOM19.952
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]
1.03-0.23-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.804
r_dihedral_angle_4_deg16.349
r_dihedral_angle_3_deg12.09
r_dihedral_angle_1_deg5.853
r_scangle_it5.594
r_scbond_it4.056
r_mcangle_it2.577
r_mcbond_it2.347
r_angle_refined_deg1.33
r_angle_other_deg0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.804
r_dihedral_angle_4_deg16.349
r_dihedral_angle_3_deg12.09
r_dihedral_angle_1_deg5.853
r_scangle_it5.594
r_scbond_it4.056
r_mcangle_it2.577
r_mcbond_it2.347
r_angle_refined_deg1.33
r_angle_other_deg0.805
r_mcbond_other0.586
r_nbd_refined0.216
r_symmetry_vdw_refined0.194
r_nbtor_refined0.185
r_nbd_other0.178
r_symmetry_vdw_other0.172
r_symmetry_hbond_refined0.112
r_xyhbond_nbd_refined0.105
r_nbtor_other0.082
r_chiral_restr0.081
r_bond_refined_d0.011
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 Atoms10132
Nucleic Acid Atoms
Solvent Atoms777
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling