3AWN

Crystal structure of D-serine dehydratase from chicken kidney (EDTA treated)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ANU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOUR DIFFUSION, HANGING DROP, MICRO-SEEDING6.529312-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOUR DIFFUSION, HANGING DROP, MICRO-SEEDING, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8156.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.329α = 90
b = 105.329β = 90
c = 82.018γ = 90
Symmetry
Space GroupP 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702011-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

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
12.89099.912.66.91190011883
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9599.76.71675

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ANU2.82011245112455921000.212930.212930.210650.25677RANDOM24.024
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]
-0.65-0.651.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.72
r_dihedral_angle_4_deg17.202
r_dihedral_angle_3_deg17.08
r_dihedral_angle_1_deg6.126
r_scangle_it2.598
r_scbond_it1.483
r_angle_refined_deg1.433
r_mcangle_it1.136
r_mcbond_it0.602
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.72
r_dihedral_angle_4_deg17.202
r_dihedral_angle_3_deg17.08
r_dihedral_angle_1_deg6.126
r_scangle_it2.598
r_scbond_it1.483
r_angle_refined_deg1.433
r_mcangle_it1.136
r_mcbond_it0.602
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2767
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms15

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling