Experiment: 2QDQ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	292	100 mM Citrate buffer (pH 4.2), 11% (w/v) PEG 3000, 200 mM Sodium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.82	α = 90
b = 98.82	β = 90
c = 98.82	γ = 90

Symmetry
Space Group	P 41 3 2

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 315		2006-11-06	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.07225	ESRF	ID23-1
2	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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
1,2	2.2	30	99.9	0.057	51.71	39.9	8844	8844		-3	50.658

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)
	2.2	2.33	100		0.531	9.2	41.7	1373

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	2.2	29.8	8396	8396	442	100	0.257	0.257	0.257	0.315	RANDOM	49.298

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.772
r_dihedral_angle_4_deg	22.492
r_dihedral_angle_3_deg	18.027
r_dihedral_angle_1_deg	3.859
r_angle_refined_deg	1.092
r_symmetry_hbond_refined	0.307
r_nbtor_refined	0.288
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.772
r_dihedral_angle_4_deg	22.492
r_dihedral_angle_3_deg	18.027
r_dihedral_angle_1_deg	3.859
r_angle_refined_deg	1.092
r_symmetry_hbond_refined	0.307
r_nbtor_refined	0.288
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	548
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

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.