Experiment: 2GYW

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J06	PDB ENTRY 1J06

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	278	26-30 % PEG750MME, 0.1 M HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
4.19	70.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.06	α = 90
b = 111.53	β = 90
c = 227.36	γ = 90

Symmetry
Space Group	P 21 21 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		2006-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-5	1.07962	MAX II	I911-5

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	2.4	29.67	99.9	0.088	16.8	7.4		79454

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	2.4	2.53	100		0.554	4.4	7.5	11478

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1J06	2.4	29.67	79374	1568	100	0.197	0.197	0.196	0.232	RANDOM	43.651

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]
0.26			0.33		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.922
r_dihedral_angle_4_deg	19.549
r_dihedral_angle_3_deg	17.142
r_dihedral_angle_1_deg	6.385
r_scangle_it	2.87
r_scbond_it	1.761
r_angle_refined_deg	1.444
r_mcangle_it	1.085
r_mcbond_it	0.634
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.922
r_dihedral_angle_4_deg	19.549
r_dihedral_angle_3_deg	17.142
r_dihedral_angle_1_deg	6.385
r_scangle_it	2.87
r_scbond_it	1.761
r_angle_refined_deg	1.444
r_mcangle_it	1.085
r_mcbond_it	0.634
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.277
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.161
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8336
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	121

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

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.