2EPL

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtheraccompanying SeMet structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.1293100mM Tris, 2M ammonium sulphate, 2 %(v/v) PEG400, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9368.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.561α = 90
b = 124.535β = 90
c = 147.793γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97928APS23-ID-D

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
11.429.499.880.0917.89.82221352218683318.5
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)
11.41.4499.390.52.537.3

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 REPLACEMENTTHROUGHOUTaccompanying SeMet structure1.429.392218682107801108899.880.186990.186990.186350.19905RANDOM20.709
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]
-1.8-1.092.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_4_deg16.711
r_dihedral_angle_3_deg11.834
r_dihedral_angle_1_deg5.79
r_scangle_it5.594
r_scbond_it4.052
r_mcangle_it2.574
r_mcbond_it2.338
r_angle_refined_deg1.304
r_angle_other_deg0.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_4_deg16.711
r_dihedral_angle_3_deg11.834
r_dihedral_angle_1_deg5.79
r_scangle_it5.594
r_scbond_it4.052
r_mcangle_it2.574
r_mcbond_it2.338
r_angle_refined_deg1.304
r_angle_other_deg0.814
r_mcbond_other0.492
r_symmetry_vdw_other0.251
r_symmetry_vdw_refined0.244
r_symmetry_hbond_refined0.223
r_nbd_refined0.212
r_nbtor_refined0.185
r_nbd_other0.174
r_xyhbond_nbd_refined0.123
r_chiral_restr0.08
r_nbtor_other0.08
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 Atoms4992
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling