2IXA

A-zyme, N-acetylgalactosaminidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.2546-50% 2-METHYL-2,4-PENTANEDIOL (MPD), 75 MM NA-CITRATE PH 6.25
Crystal Properties
Matthews coefficientSolvent content
3.4465

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.659α = 90
b = 87.659β = 90
c = 299.427γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.350980.0825.711.33065242.77
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)
12.32.3682.80.494.58.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.347.0429418123497.80.1930.1920.22RANDOM45.07
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]
2.551.282.55-3.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.903
r_dihedral_angle_4_deg19.673
r_dihedral_angle_3_deg17.574
r_dihedral_angle_1_deg5.636
r_scangle_it1.153
r_mcangle_it1.144
r_angle_refined_deg1.141
r_mcbond_it0.916
r_angle_other_deg0.855
r_scbond_it0.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.903
r_dihedral_angle_4_deg19.673
r_dihedral_angle_3_deg17.574
r_dihedral_angle_1_deg5.636
r_scangle_it1.153
r_mcangle_it1.144
r_angle_refined_deg1.141
r_mcbond_it0.916
r_angle_other_deg0.855
r_scbond_it0.825
r_symmetry_vdw_other0.206
r_nbd_other0.191
r_nbtor_refined0.175
r_nbd_refined0.174
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.133
r_nbtor_other0.085
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3402
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing