5AEE

A bacterial protein structure in glycoside hydrolase family 31


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AEDPDB ENTRY 5AED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529325 MG/ML-1 PROTEIN IN 50 MM NAPO4 , PH6.5, AND 250 MM NACL BUFFER IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1-0.15 M CACL2, AND 20 DEGREE
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.96α = 90
b = 107.62β = 107.85
c = 103.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193PIXELDECTRIS PILATUS 6M2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.8553.81880.0513.53.4121021-330.7
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)
11.851.972.90.881.22.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5AED1.8553.81114918605287.520.164460.162530.2009RANDOM32.28
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]
0.250.61-0.760.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.65
r_dihedral_angle_4_deg16.055
r_dihedral_angle_3_deg14.263
r_dihedral_angle_1_deg7.281
r_scbond_it3.546
r_mcangle_it3.542
r_mcbond_it2.595
r_mcbond_other2.593
r_angle_refined_deg1.87
r_angle_other_deg1.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.65
r_dihedral_angle_4_deg16.055
r_dihedral_angle_3_deg14.263
r_dihedral_angle_1_deg7.281
r_scbond_it3.546
r_mcangle_it3.542
r_mcbond_it2.595
r_mcbond_other2.593
r_angle_refined_deg1.87
r_angle_other_deg1.056
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
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_mcangle_other
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 Atoms10741
Nucleic Acid Atoms
Solvent Atoms602
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
REFMACphasing