4NXK

Crystal structure of Abp-D197A, a catalytic mutant of a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NX0 

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
3.8467.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.701α = 90
b = 203.525β = 90
c = 286.946γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-09-11MSINGLE 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
12.324.8697.1269263255755
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)
12.32.3496.320.0868.35.5

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NX02.324.862692632557551361196.320.171090.171090.169530.20069RANDOM36.362
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]
-3.094.21-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.285
r_dihedral_angle_4_deg17.201
r_dihedral_angle_3_deg15.587
r_dihedral_angle_1_deg6.94
r_angle_refined_deg1.841
r_angle_other_deg1.722
r_chiral_restr0.13
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_bond_other_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.285
r_dihedral_angle_4_deg17.201
r_dihedral_angle_3_deg15.587
r_dihedral_angle_1_deg6.94
r_angle_refined_deg1.841
r_angle_other_deg1.722
r_chiral_restr0.13
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_bond_other_d0.013
r_gen_planes_other0.011
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms27776
Nucleic Acid Atoms
Solvent Atoms3062
Heterogen Atoms588

Software

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