2AXQ

Apo histidine-tagged saccharopine dehydrogenase (L-Glu forming) from Saccharomyces cerevisiae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	1.2M Ammonium sulfate, 25mM Bis-Tris, 6.5-7mg/mL enzyme, 50mM Tris-HCl pH 8.0, 150mM KCl, 75mM imidazole, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.279	α = 90
b = 85.279	β = 90
c = 141.977	γ = 120

Symmetry
Space Group	P 31 2 1

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	2003-08-18	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	1.7	39.85	97.6	0.056	15.8	7.18	66370	64775		2	23.6

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)
	1.7	1.76	95.9	95.9	0.368	4.3	4.98	6559

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 1E5L, used monomer, backbone only	1.7	39.85	2	64787	64774	3290	97.6	0.2	0.2	0.198	0.24	RANDOM	27.461

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.542
r_dihedral_angle_4_deg	15.705
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.483
r_mcangle_it	3.409
r_scbond_it	2.709
r_mcbond_it	2.506
r_angle_refined_deg	1.407
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.542
r_dihedral_angle_4_deg	15.705
r_dihedral_angle_3_deg	13.158
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.483
r_mcangle_it	3.409
r_scbond_it	2.709
r_mcbond_it	2.506
r_angle_refined_deg	1.407
r_nbtor_refined	0.311
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.129
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3444
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	20

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CCP4	data scaling
ARP/wARP	model building
XTALVIEW	refinement

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.