2QRJ | pdb_00002qrj

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q99	PDB ENTRY 2Q99 (BACKBONE ONLY)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	PEG-MME 2000, Tris, (NH4)2SO4, pH 7.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.628	α = 90
b = 55.206	β = 116.24
c = 75.039	γ = 90

Symmetry
Space Group	C 1 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	2005-11-08	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	1.6	28.75	97.1	0.06	11.3	6.71	54642	53059	2	2	33.9

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)
	1.6	1.66	92.9		0.477	3	5.57	5040

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Q99 (BACKBONE ONLY)	1.6	30	54642	53011	2704	97.02	0.223	0.223	0.221	0.22	0.26	0.25	RANDOM	29.498

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]
-0.47		1.03	-0.02		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.699
r_dihedral_angle_4_deg	17.745
r_dihedral_angle_3_deg	14.185
r_dihedral_angle_1_deg	5.781
r_scangle_it	2.595
r_mcangle_it	2.462
r_scbond_it	1.945
r_mcbond_it	1.799
r_angle_refined_deg	1.474
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.699
r_dihedral_angle_4_deg	17.745
r_dihedral_angle_3_deg	14.185
r_dihedral_angle_1_deg	5.781
r_scangle_it	2.595
r_mcangle_it	2.462
r_scbond_it	1.945
r_mcbond_it	1.799
r_angle_refined_deg	1.474
r_nbtor_refined	0.3
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2864
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	16

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 R01GM157729.