Experiment: 3UP5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UOY	PDB ENTRY 3UOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	22% PEG3350, 0.1 M sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.837	α = 90
b = 94.394	β = 102.38
c = 93.135	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX-300		2010-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

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	2.453	90.968	96.6	0.097	9.2	2.7		39964

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	2.453	2.54	98.2		0.349		2.6	4025

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3UOY	2.453	48.353	39933	2017	96.22	0.1874	0.1848	0.2361	RANDOM	25.9167

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]
-1.64		-0.28	3.69		-2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.016
r_dihedral_angle_4_deg	18.954
r_dihedral_angle_3_deg	17.401
r_dihedral_angle_1_deg	7.189
r_scangle_it	3.878
r_scbond_it	2.471
r_angle_refined_deg	1.842
r_mcangle_it	1.423
r_mcbond_it	0.77
r_chiral_restr	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.016
r_dihedral_angle_4_deg	18.954
r_dihedral_angle_3_deg	17.401
r_dihedral_angle_1_deg	7.189
r_scangle_it	3.878
r_scbond_it	2.471
r_angle_refined_deg	1.842
r_mcangle_it	1.423
r_mcbond_it	0.77
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8491
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	202

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	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 R01GM157729.