Experiment: 6XT2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VL0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	278	10 mg/ml protein, 1 mM NAD+, 4 mM 1H,1H-heptafluorobutanol, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethananesulfonate, 10-25% 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.24	48.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.15	α = 90
b = 180.27	β = 105.83
c = 86.9	γ = 90

Symmetry
Space Group	P 1 21 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	AREA DETECTOR	RIGAKU	confocal	2004-04-12	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.55	19.92	88.3	0.049	0.053	20.7	5.64		188871

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.61	77.2		0.279	0.346	3.1	2.62

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	5VL0	1.55	19.84	187028	1769	88.26	0.1382	0.1377	0.15	0.1923	0.2	RANDOM	20.908

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]
1.29		0.06	-0.97		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.655
r_dihedral_angle_4_deg	13.303
r_dihedral_angle_3_deg	12.6
r_dihedral_angle_1_deg	6.854
r_rigid_bond_restr	3.498
r_angle_refined_deg	1.977
r_angle_other_deg	1.504
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.655
r_dihedral_angle_4_deg	13.303
r_dihedral_angle_3_deg	12.6
r_dihedral_angle_1_deg	6.854
r_rigid_bond_restr	3.498
r_angle_refined_deg	1.977
r_angle_other_deg	1.504
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11140
Nucleic Acid Atoms
Solvent Atoms	1238
Heterogen Atoms	296

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
PDB_EXTRACT	data extraction
d*TREK	data reduction
REFMAC	phasing

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.