Experiment: 5VJ5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JU9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	8.4	278	50 mM Tris-HCl, pH 8.4, 10 mg protein/ml in dialysis bag, dialyzed against 2-methyl-2,4-pentanediol, raised slowly to 25 %. Crystals soaked with 5 mM 1,10-phenanthroline for 2 hr at 278K, and flash vitrified in liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.28	α = 90
b = 73.41	β = 90
c = 180.8	γ = 90

Symmetry
Space Group	P 21 21 21

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++	MSC Yale confocal Osmic	2005-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	20	96.1	0.079	8.8	5.3		55508			22.5

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	94.3		0.384	2.9	3.38

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	1JU9	1.9	20	55508	1169	96.14	0.2485	0.2475	0.2954	RANDOM	35.539

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]
1.91			1.73		-3.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.668
r_dihedral_angle_4_deg	18.508
r_dihedral_angle_3_deg	17.031
r_dihedral_angle_1_deg	7.608
r_angle_refined_deg	1.807
r_angle_other_deg	1.085
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.668
r_dihedral_angle_4_deg	18.508
r_dihedral_angle_3_deg	17.031
r_dihedral_angle_1_deg	7.608
r_angle_refined_deg	1.807
r_angle_other_deg	1.085
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5568
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
O	model building
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.