3IOY

Structure of putative short-chain dehydrogenase (Saro_0793) from Novosphingobium aromaticivorans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52982.4 M Sodium Malonate pH 7.5, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.683α = 90
b = 100.753β = 101.91
c = 63.463γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-25SINGLE WAVELENGTH
21x-rayCCDADSC QUANTUM 3152009-04-25
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9793NSLSX25
2SYNCHROTRONNSLS BEAMLINE X29A0.9793NSLSX29A

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
1,21.95099.70.09113.37.249623
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)
1.91.9799.10.4756

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 DIFFRACTIONSADTHROUGHOUT1.95047074252298.760.202480.200820.23346RANDOM51.542
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]
2.26-1.5-0.91-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.503
r_dihedral_angle_4_deg21.314
r_dihedral_angle_3_deg16.247
r_dihedral_angle_1_deg5.859
r_scangle_it4.024
r_scbond_it2.443
r_mcangle_it1.614
r_angle_refined_deg1.432
r_mcbond_it0.9
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.503
r_dihedral_angle_4_deg21.314
r_dihedral_angle_3_deg16.247
r_dihedral_angle_1_deg5.859
r_scangle_it4.024
r_scbond_it2.443
r_mcangle_it1.614
r_angle_refined_deg1.432
r_mcbond_it0.9
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4189
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
CCP4phasing