Experiment: 5J16

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T0J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.2M CaCl2, 0.1M Bis-Tris pH 6.0, 18-22% (W/V) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.942	α = 105.46
b = 78.762	β = 102.28
c = 80.052	γ = 109.47

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	IMAGE PLATE	RIGAKU RAXIS IV++		2012-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	2.399	72.787	96.3	0.06	0.069	0.035	18.1	4	43376	43376

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	93.3		0.383	0.383	0.443	0.222	2	3.9	6153

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	3T0J	2.4	72.79	41180	2196	96.27	0.1837	0.1809	0.2372	RANDOM	38.021

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]
3.87	-0.42	-0.44	-1.27	-0.19	-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.952
r_dihedral_angle_4_deg	18.132
r_dihedral_angle_3_deg	17.456
r_dihedral_angle_1_deg	6.968
r_angle_refined_deg	1.703
r_angle_other_deg	1.063
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.952
r_dihedral_angle_4_deg	18.132
r_dihedral_angle_3_deg	17.456
r_dihedral_angle_1_deg	6.968
r_angle_refined_deg	1.703
r_angle_other_deg	1.063
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7740
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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 R01GM157729.