Experiment: 3G30

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	292	Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.803	α = 90
b = 41.803	β = 90
c = 230.542	γ = 120

Symmetry
Space Group	P 32 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	ADSC QUANTUM Q315r	mirrors	2008-07-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

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	1.8	50	99.7	0.09		7.4		22863		-3

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)
	1.8	1.86	98.5		0.792		5.9	2167

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	PDB entry 1YLJ	1.8	38.43	22803	1135	99.74	0.21	0.208	0.245	RANDOM	25.36

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]
0.97	0.48		0.97		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.448
r_dihedral_angle_4_deg	18.03
r_dihedral_angle_3_deg	14.164
r_dihedral_angle_1_deg	6.447
r_scangle_it	3.621
r_scbond_it	2.407
r_angle_refined_deg	1.697
r_mcangle_it	1.624
r_mcbond_it	1.091
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.448
r_dihedral_angle_4_deg	18.03
r_dihedral_angle_3_deg	14.164
r_dihedral_angle_1_deg	6.447
r_scangle_it	3.621
r_scbond_it	2.407
r_angle_refined_deg	1.697
r_mcangle_it	1.624
r_mcbond_it	1.091
r_nbtor_refined	0.302
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.176
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1997
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	51

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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 R01GM133198.