5U2W

Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V2GPDB entry 3v2g via Balbes

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290Molecular Dimensions Morpheus screen G2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate: 100mM MES/imidazole pH 6.5: BuceA.00010.g.B1.PW37236 at 20.78mg/ml + 4mM NADP: cryo: direct: tray 285571g2, puck yrq2-3
Crystal Properties
Matthews coefficientSolvent content
2.3547.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.97α = 90
b = 72.37β = 100.88
c = 100.53γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.5543.945980.047138.6514.301137073-310.88
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5990.40.390.9116.018.30912623

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 3v2g via Balbes1.5543.9451.34137043201998.040.13730.13690.163215.5888
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
f_dihedral_angle_d12.951
f_angle_d1.017
f_chiral_restr0.064
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6919
Nucleic Acid Atoms
Solvent Atoms1314
Heterogen Atoms244

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction