Experiment: 3GD0

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	6.5	293	0.15M ammonium sulfate, 30% PEG MME5000, 0.1M MES (pH6.5), LIQUID DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.164	α = 90
b = 60.683	β = 90
c = 149.395	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	77	CCD	ADSC QUANTUM 210		2006-06-08	M	SINGLE WAVELENGTH
2	2	x-ray	77	CCD	ADSC QUANTUM 4		2006-06-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.9762	NSRRC	BL13C1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	0.9794, 0.9796, 0.9642	SPring-8	BL12B2

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	1.62	29.7	100	0.06	0.047	43.9	14	54287	54285	28.5	16.8	17.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.62	1.68	100		0.336	0.3	8.4	12.3	5354

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.62	29.7	51526	2760	99.97	0.18135	0.1794	0.21768	RANDOM	17.074

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]
-0.27			-0.51		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.647
r_dihedral_angle_4_deg	16.686
r_dihedral_angle_3_deg	12.943
r_dihedral_angle_1_deg	6.063
r_scangle_it	2.308
r_mcangle_it	1.864
r_scbond_it	1.516
r_angle_refined_deg	1.323
r_mcbond_it	1.079
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.647
r_dihedral_angle_4_deg	16.686
r_dihedral_angle_3_deg	12.943
r_dihedral_angle_1_deg	6.063
r_scangle_it	2.308
r_mcangle_it	1.864
r_scbond_it	1.516
r_angle_refined_deg	1.323
r_mcbond_it	1.079
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2757
Nucleic Acid Atoms
Solvent Atoms	730
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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 R01GM133198.