2QRK

Crystal Structure of AMP-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	PEG-MME 2000, Bis-Tris, AMP, pH 6.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.97	α = 90
b = 69.106	β = 90
c = 127.829	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	IMAGE PLATE	RIGAKU RAXIS IV	MICRO-OPTICS	2007-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	29.01	97.8	0.034	25.9	5.87	41931	41009	2	2	28.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.81	91.9		0.154	8.8	5.06	3799

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Q99 (BACKBONE ONLY)	1.75	30	41931	41007	2064	97.8	0.2	0.2	0.199	0.233	RANDOM	17.833

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]
			-0.06		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.402
r_dihedral_angle_4_deg	20.963
r_dihedral_angle_3_deg	14.001
r_dihedral_angle_1_deg	5.303
r_scangle_it	2.936
r_scbond_it	1.994
r_angle_refined_deg	1.412
r_mcangle_it	1.357
r_mcbond_it	0.853
r_symmetry_vdw_refined	0.347

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.402
r_dihedral_angle_4_deg	20.963
r_dihedral_angle_3_deg	14.001
r_dihedral_angle_1_deg	5.303
r_scangle_it	2.936
r_scbond_it	1.994
r_angle_refined_deg	1.412
r_mcangle_it	1.357
r_mcbond_it	0.853
r_symmetry_vdw_refined	0.347
r_nbtor_refined	0.305
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.142
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2864
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	23

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
ARP/wARP	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.