5O1O | pdb_00005o1o

Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain with proline 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	286	0.1M tris pH 7.5 -- 0.2M sodium malonate -- 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.374	α = 90
b = 102.414	β = 90
c = 142.074	γ = 90

Symmetry
Space Group	P 21 21 21

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		2017-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	2.71	83.03	100	0.113	0.998	12.6	6.6		37204			48.72

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	2.71	2.76	99.9		0.615	1.4	6.9

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	2.48	83.08	42985	2169	92.83	0.32304	0.32181	0.32	0.34754	0.35	RANDOM	61.296

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]
0.86			1.96		-2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.442
r_dihedral_angle_3_deg	10.895
r_dihedral_angle_4_deg	7.887
r_dihedral_angle_1_deg	4.082
r_long_range_B_refined	2.157
r_long_range_B_other	2.157
r_mcangle_it	1.318
r_mcangle_other	1.318
r_angle_refined_deg	0.923
r_angle_other_deg	0.81
r_scangle_other	0.752
r_mcbond_it	0.708
r_mcbond_other	0.708
r_scbond_it	0.369
r_scbond_other	0.369
r_chiral_restr	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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	6485
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	24

Software

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