5AEG | pdb_00005aeg

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 YIHQ PROTEIN STOCK 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 BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 DEGREE. THE LIGAND I5F WAS SOAKED INTO THE NATIVE CRYSTAL.
Crystal Properties
Matthews coefficientSolvent content
238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.665α = 90
b = 112.643β = 109.52
c = 111.881γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M2015-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.8549.6898.60.0513.54154198-3
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)
11.851.8895.70.622.13.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5AED1.85105.45146377757898.350.161890.160260.170.193370.2RANDOM35.762
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]
-1.70.91-2.362.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.12
r_dihedral_angle_4_deg17.534
r_dihedral_angle_3_deg14.556
r_dihedral_angle_1_deg7.259
r_mcangle_it4.164
r_scbond_it3.986
r_mcbond_it3.231
r_mcbond_other3.229
r_angle_refined_deg1.858
r_angle_other_deg1.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.12
r_dihedral_angle_4_deg17.534
r_dihedral_angle_3_deg14.556
r_dihedral_angle_1_deg7.259
r_mcangle_it4.164
r_scbond_it3.986
r_mcbond_it3.231
r_mcbond_other3.229
r_angle_refined_deg1.858
r_angle_other_deg1.077
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms10757
Nucleic Acid Atoms
Solvent Atoms724
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing