5O1N | pdb_00005o1n

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5L76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	285	25% PEG3350 -- 0.3M sodium malonate -- 0.1M tris pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.396	α = 90
b = 89.396	β = 90
c = 147.893	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2017-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.28	44.7	100	0.076	1	15.9	13.3		28144			55.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.34	100		0.758	1.3	10.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5l76	2.28	44.7	26469	1371	99.11	0.26585	0.26483	0.26	0.28559	0.28	RANDOM	68.328

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]
2.58			2.58		-5.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.176
r_dihedral_angle_4_deg	11.686
r_dihedral_angle_3_deg	11.168
r_dihedral_angle_1_deg	4.833
r_long_range_B_refined	3.492
r_long_range_B_other	3.492
r_mcangle_it	2.209
r_mcangle_other	2.209
r_scangle_other	1.684
r_mcbond_it	1.225
r_mcbond_other	1.225
r_angle_refined_deg	0.997
r_scbond_it	0.938
r_scbond_other	0.935
r_angle_other_deg	0.835
r_chiral_restr	0.055
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	3284
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing