Experiment: 4Y9L

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	PEG 3350, Tris, magnesium formate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.925	α = 90
b = 113.396	β = 123.98
c = 113.901	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	RAYONIX MX-225		2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.99985	SSRF	BL17U

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	2.27	50	98.9	0.11	11.6	7.2	67044	66307			46.9

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	2.27	2.31	83.6		0.394	4.1	4.5

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	3DJL	2.27	50	63003	3260	98.68	0.1698	0.167	0.2229	RANDOM	52.063

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]
0.18		-0.01	-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.214
r_dihedral_angle_4_deg	20.019
r_dihedral_angle_3_deg	15.641
r_dihedral_angle_1_deg	6.66
r_mcangle_it	2.255
r_angle_refined_deg	1.817
r_mcbond_it	1.442
r_mcbond_other	1.441
r_angle_other_deg	0.86
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.214
r_dihedral_angle_4_deg	20.019
r_dihedral_angle_3_deg	15.641
r_dihedral_angle_1_deg	6.66
r_mcangle_it	2.255
r_angle_refined_deg	1.817
r_mcbond_it	1.442
r_mcbond_other	1.441
r_angle_other_deg	0.86
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9235
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	106

Software

Software
Software Name	Purpose
HKL-2000	data processing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

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 R01GM133198.