3KBO

2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING DROP, temperature 295K; Cryo: oil, paratone
Crystal Properties
Matthews coefficientSolvent content
2.4549.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 279.621α = 90
b = 45.585β = 101.58
c = 112.335γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2009-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.143098.20.084276.67571075710-334.7
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)
12.142.1893.50.4913.563610

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.1429.9371864718643806980.213870.213870.210920.26879RANDOM27.209
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]
-1.570.235.13-3.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.664
r_dihedral_angle_3_deg11.693
r_dihedral_angle_4_deg10.682
r_scangle_it4.87
r_scbond_it3.469
r_dihedral_angle_1_deg2.762
r_mcangle_it2.147
r_angle_refined_deg1.453
r_mcbond_it1.286
r_angle_other_deg0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.664
r_dihedral_angle_3_deg11.693
r_dihedral_angle_4_deg10.682
r_scangle_it4.87
r_scbond_it3.469
r_dihedral_angle_1_deg2.762
r_mcangle_it2.147
r_angle_refined_deg1.453
r_mcbond_it1.286
r_angle_other_deg0.87
r_mcbond_other0.375
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9900
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms243

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing