5O1N

Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain with N-[(2S)-2-Pyrrolidinylmethyl]-trifluoromethanesulfonamide bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528525% PEG3350 -- 0.3M sodium malonate -- 0.1M tris pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.2261.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.396α = 90
b = 89.396β = 90
c = 147.893γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

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
12.2844.71000.076115.913.32814455.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.341000.7581.310.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5l762.2844.726469137199.110.265850.264830.28559RANDOM68.328
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]
2.582.58-5.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.176
r_dihedral_angle_4_deg11.686
r_dihedral_angle_3_deg11.168
r_dihedral_angle_1_deg4.833
r_long_range_B_refined3.492
r_long_range_B_other3.492
r_mcangle_it2.209
r_mcangle_other2.209
r_scangle_other1.684
r_mcbond_it1.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.176
r_dihedral_angle_4_deg11.686
r_dihedral_angle_3_deg11.168
r_dihedral_angle_1_deg4.833
r_long_range_B_refined3.492
r_long_range_B_other3.492
r_mcangle_it2.209
r_mcangle_other2.209
r_scangle_other1.684
r_mcbond_it1.225
r_mcbond_other1.225
r_angle_refined_deg0.997
r_scbond_it0.938
r_scbond_other0.935
r_angle_other_deg0.835
r_chiral_restr0.055
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3284
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing