Experiment: 2GD5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	8-12% PEG 3350, 200mM ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.58	α = 68.68
b = 72.57	β = 83.61
c = 89.23	γ = 76.7

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 4r		2005-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97927	ESRF	ID14-4

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	2.8	33	94.7	0.096	14.33			17853		-3	63.075

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	2.8	3	94.8		0.464	4.98

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.8	20	18713	16944	909	95.68	0.26106	0.25883	0.30106	RANDOM	59.707

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]
4.86	1.09	0.25	-5.72	-2.36	2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.61
r_dihedral_angle_3_deg	19.328
r_dihedral_angle_4_deg	18.93
r_dihedral_angle_1_deg	4.583
r_scangle_it	3.829
r_scbond_it	2.408
r_mcangle_it	1.577
r_angle_refined_deg	1.511
r_mcbond_it	1.014
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.61
r_dihedral_angle_3_deg	19.328
r_dihedral_angle_4_deg	18.93
r_dihedral_angle_1_deg	4.583
r_scangle_it	3.829
r_scbond_it	2.408
r_mcangle_it	1.577
r_angle_refined_deg	1.511
r_mcbond_it	1.014
r_nbtor_refined	0.321
r_nbd_refined	0.303
r_symmetry_vdw_refined	0.301
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.087
r_symmetry_hbond_refined	0.044
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4746
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
SHELXS	phasing

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.