4N2R

Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maydis in complex with L-arabinofuranose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N1IPDB entry 4N1I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP528520% (w/v) PEG 3350 0.2 M Sodium phosphate 0.05 M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K
Crystal Properties
Matthews coefficientSolvent content
1.8232.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.08α = 90
b = 66.07β = 90
c = 68.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102012-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93340ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.25095.90.026354.385293817631-312.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2389.90.1439.354.25597

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4N1I1.247.4218176377664409895.850.101180.099650.13016RANDOM10.908
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]
-0.010.04-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.944
r_dihedral_angle_2_deg29.774
r_dihedral_angle_4_deg25.815
r_dihedral_angle_3_deg11.796
r_sphericity_bonded10.793
r_dihedral_angle_1_deg7.884
r_rigid_bond_restr6.109
r_long_range_B_refined4.768
r_long_range_B_other3.877
r_scangle_other3.328
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.944
r_dihedral_angle_2_deg29.774
r_dihedral_angle_4_deg25.815
r_dihedral_angle_3_deg11.796
r_sphericity_bonded10.793
r_dihedral_angle_1_deg7.884
r_rigid_bond_restr6.109
r_long_range_B_refined4.768
r_long_range_B_other3.877
r_scangle_other3.328
r_scbond_it2.813
r_scbond_other2.809
r_mcbond_it2.692
r_mcangle_other2.679
r_mcangle_it2.671
r_mcbond_other2.669
r_angle_refined_deg2.117
r_angle_other_deg0.98
r_chiral_restr0.128
r_bond_refined_d0.022
r_gen_planes_refined0.012
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2376
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms29

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling