Experiment: 4X1B

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	0.1M PIPES, 17% PEG3350, 18% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.056	α = 90
b = 156.649	β = 90
c = 107.162	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	CCD	ADSC QUANTUM 315r		2012-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97852	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.45	50	99.9	0.075	0.081	0.03	10.4	7.4		42808

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.54	100		0.737	0.792	0.289	0.905		7.5	4210

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QYT	2.45	50	39358	2074	97.06	0.1918	0.19	0.19	0.2265	0.23	RANDOM	55.587

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]
-0.8			0.15		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.962
r_dihedral_angle_4_deg	18.297
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_1_deg	6.119
r_mcangle_it	1.967
r_mcbond_it	1.189
r_angle_refined_deg	1.188
r_mcbond_other	1.188
r_angle_other_deg	0.778
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.962
r_dihedral_angle_4_deg	18.297
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_1_deg	6.119
r_mcangle_it	1.967
r_mcbond_it	1.189
r_angle_refined_deg	1.188
r_mcbond_other	1.188
r_angle_other_deg	0.778
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5045
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	14

Software

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