Experiment: 2QDN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	15% PEG 3350, 0.1 M Succinic acid pH 7.0, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.923	α = 90
b = 71.514	β = 90
c = 70.188	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	CCD	ADSC QUANTUM 4		2006-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	1.74332	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.09	50.06	90.3	0.043	0.048	27.3	11.2	14872	14872

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	2.09	2.16	52.9		0.121		6	1611

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.09	50.06	14834	14834	750	90.2	0.177	0.177	0.174	0.229	RANDOM	21.558

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]
0.81			0.56		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.942
r_dihedral_angle_3_deg	14.582
r_dihedral_angle_1_deg	7.708
r_scangle_it	3.315
r_scbond_it	2.166
r_angle_refined_deg	1.372
r_mcangle_it	1.338
r_mcbond_it	0.839
r_nbtor_refined	0.306
r_nbd_refined	0.193

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.942
r_dihedral_angle_3_deg	14.582
r_dihedral_angle_1_deg	7.708
r_scangle_it	3.315
r_scbond_it	2.166
r_angle_refined_deg	1.372
r_mcangle_it	1.338
r_mcbond_it	0.839
r_nbtor_refined	0.306
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.143
r_symmetry_vdw_refined	0.134
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1982
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.