3DXV

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SFTPDB ENTRY 1SFT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.729325% PEG4000, 0.17M magnesium chloride, 0.08M Tris/HCl (pH8.7), 5% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8633.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.547α = 90
b = 61.063β = 103.22
c = 105.227γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.215099.60.1080.0745.935281
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.2998.20.4940.4295.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SFT2.2119.963528133451176599.630.199760.197340.24522RANDOM30.541
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.533
r_dihedral_angle_4_deg19.198
r_dihedral_angle_3_deg17.617
r_dihedral_angle_1_deg5.463
r_scangle_it2.197
r_scbond_it1.324
r_angle_refined_deg1.274
r_mcangle_it0.907
r_mcbond_it0.528
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.533
r_dihedral_angle_4_deg19.198
r_dihedral_angle_3_deg17.617
r_dihedral_angle_1_deg5.463
r_scangle_it2.197
r_scbond_it1.324
r_angle_refined_deg1.274
r_mcangle_it0.907
r_mcbond_it0.528
r_nbtor_refined0.302
r_symmetry_vdw_refined0.205
r_nbd_refined0.2
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.115
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6325
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms30

Software

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