3ANU

Crystal structure of D-serine dehydratase from chicken kidney


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529312-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7555.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.578α = 90
b = 104.578β = 90
c = 81.449γ = 90
Symmetry
Space GroupP 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2010-03-12MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000, 1.28179, 1.28284, 1.25510, 1.30300Photon FactoryBL-5A

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
11.91799.226.56.93620935919
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.73.56.75021

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 DIFFRACTIONMADTHROUGHOUT1.917341233412317961000.190350.190350.189060.21486RANDOM35.334
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]
-1.4-1.42.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.414
r_dihedral_angle_4_deg16.255
r_dihedral_angle_3_deg14.882
r_dihedral_angle_1_deg5.873
r_scangle_it3.108
r_scbond_it1.894
r_angle_refined_deg1.309
r_mcangle_it1.176
r_mcbond_it0.647
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.414
r_dihedral_angle_4_deg16.255
r_dihedral_angle_3_deg14.882
r_dihedral_angle_1_deg5.873
r_scangle_it3.108
r_scbond_it1.894
r_angle_refined_deg1.309
r_mcangle_it1.176
r_mcbond_it0.647
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2778
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms17

Software

Software
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling