Experiment: 5EYM

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	18 % PEG 4000, 100 mM Tris, 300 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.76	α = 90
b = 78.76	β = 90
c = 223.412	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	PIXEL	PSI PILATUS 6M		2011-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.7	68.21	97.2	0.16	0.12	5.5	2.6		20634

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	2.7	2.89	97.4		0.7	1.1	2.6

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	3EQC	2.7	68.21	19120	1357	99.24	0.2468	0.2426	0.3077	RANDOM	19.644

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]
5.01	2.5		5.01		-7.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.537
r_dihedral_angle_4_deg	13.889
r_dihedral_angle_3_deg	13.626
r_dihedral_angle_1_deg	5.407
r_scangle_it	3.863
r_scbond_it	2.458
r_mcangle_it	1.773
r_angle_other_deg	1.252
r_mcbond_it	0.972
r_angle_refined_deg	0.901

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.537
r_dihedral_angle_4_deg	13.889
r_dihedral_angle_3_deg	13.626
r_dihedral_angle_1_deg	5.407
r_scangle_it	3.863
r_scbond_it	2.458
r_mcangle_it	1.773
r_angle_other_deg	1.252
r_mcbond_it	0.972
r_angle_refined_deg	0.901
r_mcbond_other	0.124
r_chiral_restr	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2308
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

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.