Experiment: 3GR4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GQY	isomorphous replacement with pdb entry 3GQY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	20% PEG3350, 0.2M diammonium tartrate, 0.005M activator, 0.005M ADP, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.275	α = 90
b = 153.206	β = 102.91
c = 93.138	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2009-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-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	1.6	50	96.3	0.059	10.2	3.6		283418

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)
	1.6	1.66	75.2		0.707		2.5	22112

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		THROUGHOUT	isomorphous replacement with pdb entry 3GQY	1.6	30	280370	2916	96.273	0.208	0.208	0.231	thin shells (sftools)	20.294

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]
-0.546		-0.94	-0.011		0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.875
r_dihedral_angle_4_deg	15.465
r_dihedral_angle_3_deg	11.864
r_dihedral_angle_1_deg	5.375
r_scangle_it	2.803
r_mcangle_it	2.239
r_scbond_it	1.802
r_mcbond_it	1.483
r_angle_refined_deg	1.348
r_angle_other_deg	0.889

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.875
r_dihedral_angle_4_deg	15.465
r_dihedral_angle_3_deg	11.864
r_dihedral_angle_1_deg	5.375
r_scangle_it	2.803
r_mcangle_it	2.239
r_scbond_it	1.802
r_mcbond_it	1.483
r_angle_refined_deg	1.348
r_angle_other_deg	0.889
r_mcbond_other	0.434
r_chiral_restr	0.079
r_bond_refined_d	0.015
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	15294
Nucleic Acid Atoms
Solvent Atoms	917
Heterogen Atoms	292

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
MolProbity	model building
prodrg	refinement

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.