4XWH

Crystal structure of the human N-acetyl-alpha-glucosaminidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VCC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52911.0 M lithium sulfate, 0.01 M nickel chloride, 0.1 M Tris
Crystal Properties
Matthews coefficientSolvent content
5.9479.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 205.088α = 90
b = 205.088β = 90
c = 78.398γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
12.321001000.08620.79.58174045.2
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)
12.322.499.80.7631.855.8

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 REPLACEMENTTHROUGHOUT2VCC2.3210077480399399.560.16690.165910.18579RANDOM53.533
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]
0.070.040.07-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.31
r_dihedral_angle_4_deg19.703
r_dihedral_angle_3_deg18.275
r_dihedral_angle_1_deg6.162
r_long_range_B_refined5.717
r_long_range_B_other5.695
r_scangle_other3.779
r_scbond_it2.375
r_scbond_other2.374
r_mcangle_it2.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.31
r_dihedral_angle_4_deg19.703
r_dihedral_angle_3_deg18.275
r_dihedral_angle_1_deg6.162
r_long_range_B_refined5.717
r_long_range_B_other5.695
r_scangle_other3.779
r_scbond_it2.375
r_scbond_other2.374
r_mcangle_it2.239
r_mcangle_other2.239
r_angle_refined_deg1.776
r_mcbond_other1.461
r_mcbond_it1.46
r_angle_other_deg1.11
r_chiral_restr0.127
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5693
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms175

Software

Software
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction