2UZ1

1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-methyl- 2,4-pentanediol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AG0PDB ENTRY 2AG0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION 5 MG ML-1 WITH A THREEFOLD STOICHIOMETRIC EXCESS OF THIAMINE DIPHOSPHATE (THDP).
Crystal Properties
Matthews coefficientSolvent content
137

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.462α = 90
b = 121.601β = 90
c = 162.957γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.6550990.135.55.1249612
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)
11.651.681000.881.55

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 2AG01.6597.592368751253499.70.1680.1670.192RANDOM12.59
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]
-0.320.75-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.238
r_dihedral_angle_4_deg18.7
r_dihedral_angle_3_deg12.38
r_dihedral_angle_1_deg5.608
r_scangle_it2.877
r_scbond_it1.835
r_angle_refined_deg1.27
r_mcangle_it0.967
r_mcbond_it0.561
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.238
r_dihedral_angle_4_deg18.7
r_dihedral_angle_3_deg12.38
r_dihedral_angle_1_deg5.608
r_scangle_it2.877
r_scbond_it1.835
r_angle_refined_deg1.27
r_mcangle_it0.967
r_mcbond_it0.561
r_nbtor_refined0.303
r_nbd_refined0.202
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.178
r_xyhbond_nbd_refined0.111
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms16184
Nucleic Acid Atoms
Solvent Atoms1881
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing