2DRW

The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.2144.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.205α = 90
b = 123.219β = 104.36
c = 115.706γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102005-05-22MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.9791, 0.9793, 0.9900SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.147.5799.21176251
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1891.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.147.57115879612499.920.185260.182170.24321RANDOM26.864
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_deg34.395
r_dihedral_angle_4_deg18.841
r_dihedral_angle_3_deg15.02
r_dihedral_angle_1_deg6.398
r_scangle_it2.428
r_scbond_it1.571
r_angle_refined_deg1.265
r_mcangle_it1.054
r_mcbond_it0.574
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.395
r_dihedral_angle_4_deg18.841
r_dihedral_angle_3_deg15.02
r_dihedral_angle_1_deg6.398
r_scangle_it2.428
r_scbond_it1.571
r_angle_refined_deg1.265
r_mcangle_it1.054
r_mcbond_it0.574
r_nbtor_refined0.302
r_metal_ion_refined0.248
r_nbd_refined0.201
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.161
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16380
Nucleic Acid Atoms
Solvent Atoms2056
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
JUPITOR210data reduction
HKL-2000data scaling
SHELXDphasing