2EPM

N-acetyl-B-D-glucoasminidase (GCNA) from Stretococcus gordonii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EPLPDB entry 2EPL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3293100mM Tris, 1.9M ammonium sulphate, 0.5%(v/v) PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9268.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.964α = 90
b = 124.746β = 90
c = 147.889γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2006-12-12MSINGLE 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
12.0414.9599.310.06418.98.172240717423326.6
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)
12.042.0994.310.353.747.1

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 2EPL2.0414.957224068128361499.310.200910.200910.1990.23699RANDOM40.635
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]
-2.4-1.413.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.656
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg12.946
r_scangle_it6.591
r_dihedral_angle_1_deg5.871
r_scbond_it5.048
r_mcangle_it3.145
r_mcbond_it2.772
r_angle_refined_deg1.245
r_angle_other_deg0.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.656
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg12.946
r_scangle_it6.591
r_dihedral_angle_1_deg5.871
r_scbond_it5.048
r_mcangle_it3.145
r_mcbond_it2.772
r_angle_refined_deg1.245
r_angle_other_deg0.764
r_mcbond_other0.68
r_symmetry_vdw_refined0.234
r_symmetry_vdw_other0.233
r_nbd_refined0.213
r_nbtor_refined0.188
r_nbd_other0.174
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.135
r_nbtor_other0.083
r_chiral_restr0.074
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 Atoms4798
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling