Experiment: 5HE0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PNK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	50 mM MES, 0.8-1.2 M sodium chloride, 8-16% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.554	α = 90
b = 239.927	β = 90
c = 208.872	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MARMOSAIC 300 mm CCD		2015-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	2.6	30	97	0.067	0.078	0.04	12.6	3.5		47002

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	2.6	2.64	86.1		0.391	0.476	0.268	0.909		2.5	2068

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4PNK	2.56	30	44643	2316	94.52	0.2048	0.2017	0.21	0.264	0.26	RANDOM	71.102

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]
1.3			-3.76		2.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.93
r_dihedral_angle_4_deg	19.979
r_dihedral_angle_3_deg	16.732
r_dihedral_angle_1_deg	7.184
r_mcangle_it	5.541
r_mcbond_it	3.53
r_mcbond_other	3.529
r_angle_refined_deg	1.646
r_angle_other_deg	0.83
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.93
r_dihedral_angle_4_deg	19.979
r_dihedral_angle_3_deg	16.732
r_dihedral_angle_1_deg	7.184
r_mcangle_it	5.541
r_mcbond_it	3.53
r_mcbond_other	3.529
r_angle_refined_deg	1.646
r_angle_other_deg	0.83
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8163
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
Coot	model building
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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.