Experiment: 3V8D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAX	pdb entry 3DAX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	291	30% PEG-400, 0.2M lithium sulfate, 0.1M trisodium citrate, pH 5.6, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.618	α = 66.33
b = 74.22	β = 75.53
c = 87.933	γ = 69.62

Symmetry
Space Group	P 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 300 mm CCD		2011-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97625	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	1.9	50	97.6	0.074	9.6	3.8		92430

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	1.9	1.97	96.4		0.848		3.7	9089

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 3DAX	1.9	50	92179	2066	97.601	0.186	0.1852	0.225	THIN SHELLS (SFTOOLS)	26.151

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]
-0.613	-0.549	-0.243	0.26	0.72	0.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.518
r_dihedral_angle_4_deg	15.459
r_dihedral_angle_3_deg	11.886
r_dihedral_angle_1_deg	5.408
r_angle_refined_deg	1.407
r_angle_other_deg	0.808
r_chiral_restr	0.061
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.518
r_dihedral_angle_4_deg	15.459
r_dihedral_angle_3_deg	11.886
r_dihedral_angle_1_deg	5.408
r_angle_refined_deg	1.407
r_angle_other_deg	0.808
r_chiral_restr	0.061
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7479
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	188

Software

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