2EPO

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSelenium methionine structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293100mM sodium citrate, 200mM ammonium acetate, 24%(v/v) PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2244.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.04α = 90
b = 112.49β = 90
c = 103.99γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.008MAX III711

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
11.5534.8896.850.09311.73.61848011701063319.9
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)
11.551.677.60.434.364.3

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 REPLACEMENTTHROUGHOUTSelenium methionine structure1.5634.88184801170106887496.850.212370.212370.210440.24926RANDOM19.128
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]
1.01-0.35-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.165
r_dihedral_angle_4_deg16.248
r_dihedral_angle_3_deg12.83
r_dihedral_angle_1_deg5.803
r_scangle_it5.743
r_scbond_it4.21
r_mcangle_it2.611
r_mcbond_it2.322
r_angle_refined_deg1.268
r_angle_other_deg0.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.165
r_dihedral_angle_4_deg16.248
r_dihedral_angle_3_deg12.83
r_dihedral_angle_1_deg5.803
r_scangle_it5.743
r_scbond_it4.21
r_mcangle_it2.611
r_mcbond_it2.322
r_angle_refined_deg1.268
r_angle_other_deg0.826
r_mcbond_other0.643
r_nbd_refined0.216
r_symmetry_vdw_refined0.209
r_nbtor_refined0.178
r_nbd_other0.171
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.116
r_symmetry_vdw_other0.101
r_nbtor_other0.079
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9974
Nucleic Acid Atoms
Solvent Atoms605
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling