Experiment: 5EYS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O4T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.784	α = 90
b = 88.784	β = 90
c = 114.31	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MAR555 FLAT PANEL	mirrors	2013-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID09	0.4104	ESRF	ID09

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	1.75	45.87	99.8	0.078	0.089	0.041	10.8	4.5	17681	17681			23.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	99.8		0.688	0.688	0.36	1	4.6	2551

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	4O4T	1.75	20	16010	862	95.18	0.1554	0.1538	0.1865	RANDOM	30.466

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]
0.05	0.02		0.05		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.694
r_dihedral_angle_4_deg	21.716
r_dihedral_angle_3_deg	14.202
r_dihedral_angle_1_deg	4.691
r_mcangle_it	4.133
r_mcbond_it	2.7
r_mcbond_other	2.648
r_angle_other_deg	2.073
r_angle_refined_deg	1.685
r_chiral_restr	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.694
r_dihedral_angle_4_deg	21.716
r_dihedral_angle_3_deg	14.202
r_dihedral_angle_1_deg	4.691
r_mcangle_it	4.133
r_mcbond_it	2.7
r_mcbond_other	2.648
r_angle_other_deg	2.073
r_angle_refined_deg	1.685
r_chiral_restr	0.116
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1175
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.