Experiment: 5IJE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IIH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	289	1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.0 M (NH4)2SO4, 5 mM ZnCl2, final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 100 mM ZnCl2 in 100 mM Tris, final pH 7.4, to final concentration of 100 mM

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.384	α = 90
b = 94.384	β = 90
c = 141.905	γ = 120

Symmetry
Space Group	P 61

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	ADSC QUANTUM 210r	MIRRORS	2015-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.282	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	50.01	99.5	0.079	0.09	0.042	12.4	4.3		27885

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	99.9		0.707	0.807	0.383	0.785		4.1	1398

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	5IIH	2.4	50.01	26459	1418	99.56	0.1985	0.1954	0.2553	RANDOM	55.396

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]
-1.11	-0.55		-1.11		3.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.848
r_dihedral_angle_4_deg	19.524
r_dihedral_angle_3_deg	13.998
r_dihedral_angle_1_deg	4.984
r_mcangle_it	3.304
r_mcbond_it	2.123
r_mcbond_other	2.123
r_angle_other_deg	1.301
r_angle_refined_deg	1.204
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.848
r_dihedral_angle_4_deg	19.524
r_dihedral_angle_3_deg	13.998
r_dihedral_angle_1_deg	4.984
r_mcangle_it	3.304
r_mcbond_it	2.123
r_mcbond_other	2.123
r_angle_other_deg	1.301
r_angle_refined_deg	1.204
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4463
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
SCALEPACK	data scaling
HKL-3000	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

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.