4NZF

Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus), in complex with arabinose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NXK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52931.8M Ammonium Sulfate, 0.1M citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.867.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.6α = 90
b = 201.505β = 90
c = 286.911γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.954ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1934.7189301393268240
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.192.2576.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NXK2.1934.713013932682401431889.040.170980.168470.21888RANDOM34.962
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]
-1.482.96-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.584
r_dihedral_angle_4_deg18.757
r_dihedral_angle_3_deg16.634
r_long_range_B_refined8.59
r_long_range_B_other8.576
r_dihedral_angle_1_deg7.527
r_scangle_other5.8
r_mcangle_it4.895
r_mcangle_other4.895
r_scbond_it3.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.584
r_dihedral_angle_4_deg18.757
r_dihedral_angle_3_deg16.634
r_long_range_B_refined8.59
r_long_range_B_other8.576
r_dihedral_angle_1_deg7.527
r_scangle_other5.8
r_mcangle_it4.895
r_mcangle_other4.895
r_scbond_it3.947
r_scbond_other3.922
r_mcbond_it3.347
r_mcbond_other3.346
r_angle_refined_deg1.988
r_angle_other_deg0.948
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms27794
Nucleic Acid Atoms
Solvent Atoms2932
Heterogen Atoms688

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling