5EIO | pdb_00005eio

Crystal structure of LysY from Thermus thermophilus complexed with NADP+ and LysW-gamma-aminoadipic semialdehyde


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OZP2OZP, 3WWL
experimental modelPDB 3WWL2OZP, 3WWL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 2000 MME, calcium acetate, NADP, HEPES-NaOH
Crystal Properties
Matthews coefficientSolvent content
2.0740.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.53α = 90
b = 83.53β = 90
c = 168.321γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.85099.40.11227.85.564110
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)
11.81.831000.492.85.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OZP, 3WWL1.836.3760465322699.420.170010.16780.180.212840.22RANDOM32.617
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
r_dihedral_angle_2_deg34.682
r_dihedral_angle_4_deg16.178
r_dihedral_angle_3_deg14.24
r_dihedral_angle_1_deg6.058
r_long_range_B_other5.41
r_long_range_B_refined5.409
r_scangle_other3.714
r_mcangle_it2.776
r_mcangle_other2.775
r_scbond_it2.358
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5703
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
HKL-2000data scaling
HKL-2000data collection
PHASERphasing