Experiment: 3UD8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2 M (NH4)HPO4, 0.1 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.243	α = 90
b = 46.178	β = 125.79
c = 96.689	γ = 90

Symmetry
Space Group	C 1 2 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 315r	mirrors	2010-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

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	2.37	78.43	95.5	0.055	0.055	14	3.4	15943	15908		5

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	2.38	2.47	78.2		0.241	0.241	3.06	2.7	1272

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1RG8	2.37	78.43	15908	14298	1610	95.47	0.21089	0.21089	0.20438	0.26999	RANDOM	44.927

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]
-2.9		-1.96	3.39		-2.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.909
r_dihedral_angle_4_deg	18.697
r_dihedral_angle_3_deg	18.136
r_dihedral_angle_1_deg	7.928
r_scangle_it	4.164
r_scbond_it	2.617
r_mcangle_it	1.906
r_angle_refined_deg	1.68
r_mcbond_it	1.018
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.909
r_dihedral_angle_4_deg	18.697
r_dihedral_angle_3_deg	18.136
r_dihedral_angle_1_deg	7.928
r_scangle_it	4.164
r_scbond_it	2.617
r_mcangle_it	1.906
r_angle_refined_deg	1.68
r_mcbond_it	1.018
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3080
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	47

Software

Software
Software Name	Purpose
HKL-2000	data collection
EPMR	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.