2B9V

Acetobacter turbidans alpha-amino acid ester hydrolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MPXpdb entry 1MPX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629315-17% PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.369α = 90
b = 275.594β = 90.11
c = 197.953γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.933ESRFID14-4

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
124085.50.091598744598744
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)
122.1167.80.341

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 REPLACEMENTTHROUGHOUTpdb entry 1MPX2405043795043792542075.390.200510.200510.198780.23477RANDOM, BUT SUCH THAT TWIN-RELATED REFLECTIONS ARE ALWAYS IN THE SAME SUBSET15.971
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]
0.09-0.05-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.467
r_dihedral_angle_4_deg14.367
r_dihedral_angle_3_deg12.349
r_scangle_it3.664
r_angle_other_deg3.386
r_dihedral_angle_1_deg2.715
r_scbond_it2.501
r_angle_refined_deg1.663
r_mcangle_it1.646
r_mcbond_it1.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.467
r_dihedral_angle_4_deg14.367
r_dihedral_angle_3_deg12.349
r_scangle_it3.664
r_angle_other_deg3.386
r_dihedral_angle_1_deg2.715
r_scbond_it2.501
r_angle_refined_deg1.663
r_mcangle_it1.646
r_mcbond_it1.066
r_symmetry_vdw_other0.417
r_symmetry_vdw_refined0.3
r_symmetry_hbond_other0.296
r_nbd_other0.234
r_nbd_refined0.196
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.123
r_nbtor_other0.114
r_chiral_restr0.105
r_xyhbond_nbd_other0.081
r_bond_refined_d0.008
r_gen_planes_other0.004
r_gen_planes_refined0.003
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms77056
Nucleic Acid Atoms
Solvent Atoms3654
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing