Experiment: 4W7W

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1 M sodium cacodylate, 0.2 M sodium acetate, 28% PEG8000, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.874	α = 90
b = 82.018	β = 90
c = 48.253	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 225 mm CCD		2013-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	0.918	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.05		99.8	0.109	0.12	11.28			148263		-3	11.349

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.11	99.3		1.172	1.29	1.75

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1GZJ	1.05	41.01	7409	99.83	0.1415	0.1405	0.1601	RANDOM	11.705

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]
-0.16			-0.11		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.911
r_sphericity_free	37.421
r_dihedral_angle_4_deg	27.212
r_dihedral_angle_3_deg	12.102
r_sphericity_bonded	9.29
r_dihedral_angle_1_deg	6.138
r_rigid_bond_restr	1.874
r_angle_refined_deg	1.367
r_mcangle_it	1.275
r_mcbond_it	0.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.911
r_sphericity_free	37.421
r_dihedral_angle_4_deg	27.212
r_dihedral_angle_3_deg	12.102
r_sphericity_bonded	9.29
r_dihedral_angle_1_deg	6.138
r_rigid_bond_restr	1.874
r_angle_refined_deg	1.367
r_mcangle_it	1.275
r_mcbond_it	0.939
r_mcbond_other	0.933
r_angle_other_deg	0.813
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2447
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XSCALE	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.