Experiment: 4X69

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IYS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.533	α = 90
b = 72.982	β = 109.29
c = 63.052	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	95	CCD	ADSC QUANTUM 210		2013-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.42	50	98.1	0.07	0.07	24.195	3.6		81658		-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	1.42	1.44	80.5		0.455	0.455	2.173	2.4

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	1IYS	1.42	50	77420	4113	98.18	0.1848	0.1835	0.2085	RANDOM	12.367

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]
-0.25		0.1	-0.37		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.379
r_dihedral_angle_3_deg	11.442
r_dihedral_angle_4_deg	10.445
r_dihedral_angle_1_deg	6.017
r_scangle_it	3.018
r_scbond_it	1.789
r_angle_refined_deg	1.276
r_mcangle_it	1.053
r_mcbond_it	0.575
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.379
r_dihedral_angle_3_deg	11.442
r_dihedral_angle_4_deg	10.445
r_dihedral_angle_1_deg	6.017
r_scangle_it	3.018
r_scbond_it	1.789
r_angle_refined_deg	1.276
r_mcangle_it	1.053
r_mcbond_it	0.575
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3952
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
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.