Experiment: 3K5T

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C10	PDB entry 2c10

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	298	0.1 M MES (pH 6.1), 12% w/v PEG 20,000, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.771	α = 90
b = 96.954	β = 90
c = 178.06	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC MIRRORS	2007-01-11	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210r		2008-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418
2	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.957	Australian Synchrotron	MX1

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	2.106	178.06	95.2	0.111	0.111	15.7	7.4		45200			25.3

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	2.1	2.21	96.2		0.299	0.299	2.5	3	6562

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 2c10	2.11	89.09	45199	45199	2288	94.55	0.239	0.239	0.236	0.29	RANDOM	26.043

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]
-1.95			-1.74		3.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.806
r_dihedral_angle_4_deg	15.268
r_dihedral_angle_3_deg	13.578
r_dihedral_angle_1_deg	6.739
r_scangle_it	1.792
r_angle_refined_deg	1.224
r_scbond_it	1.136
r_angle_other_deg	0.82
r_mcangle_it	0.777
r_mcbond_it	0.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.806
r_dihedral_angle_4_deg	15.268
r_dihedral_angle_3_deg	13.578
r_dihedral_angle_1_deg	6.739
r_scangle_it	1.792
r_angle_refined_deg	1.224
r_scbond_it	1.136
r_angle_other_deg	0.82
r_mcangle_it	0.777
r_mcbond_it	0.431
r_mcbond_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5587
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	79

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	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.