Experiment: 5DYK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	0.4M L-Proline, 10% Peg 3350, 0.1M Hepes 7.8 15% EG

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.509	α = 90
b = 127.284	β = 90
c = 215.104	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	ADSC QUANTUM 315		2013-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	2.45	40	96.6	0.093	8.3	4.7		47350

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	2.45	2.49	93.1		0.935		4.4	2253

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	4MYI	2.45	40	44059	2346	96.68	0.2061	0.2043	0.2405	RANDOM	51.717

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]
2.04			1.31		-3.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.031
r_dihedral_angle_4_deg	16.203
r_dihedral_angle_3_deg	13.539
r_dihedral_angle_1_deg	5.48
r_sphericity_bonded	4.02
r_rigid_bond_restr	1.689
r_mcangle_it	1.17
r_angle_refined_deg	1.151
r_angle_other_deg	0.871
r_mcbond_it	0.857

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.031
r_dihedral_angle_4_deg	16.203
r_dihedral_angle_3_deg	13.539
r_dihedral_angle_1_deg	5.48
r_sphericity_bonded	4.02
r_rigid_bond_restr	1.689
r_mcangle_it	1.17
r_angle_refined_deg	1.151
r_angle_other_deg	0.871
r_mcbond_it	0.857
r_mcbond_other	0.857
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6345
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	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.