Experiment: 4YYK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M MES, pH 6.5, 15% w/v PEG550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.84	α = 89.88
b = 34.73	β = 89.81
c = 129.08	γ = 69.45

Symmetry
Space Group	P 1

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		2012-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.68	50	96.6	0.089	13	3.7	38297	36333

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	1.68	1.74	99.9		0.617		3.1	2412

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	PDB entry 3HME	1.79	32.27	34482	1851	94.87	0.2271	0.2252	0.2	0.2612	0.23	RANDOM	29.101

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]
-1.52	-0.84	0.2	8.16	-2.82	-6.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.941
r_dihedral_angle_4_deg	24.631
r_dihedral_angle_3_deg	20.322
r_dihedral_angle_1_deg	7.772
r_mcangle_it	3.973
r_scbond_it	3.56
r_mcbond_it	3.122
r_angle_refined_deg	2.846
r_chiral_restr	0.21
r_bond_refined_d	0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.941
r_dihedral_angle_4_deg	24.631
r_dihedral_angle_3_deg	20.322
r_dihedral_angle_1_deg	7.772
r_mcangle_it	3.973
r_scbond_it	3.56
r_mcbond_it	3.122
r_angle_refined_deg	2.846
r_chiral_restr	0.21
r_bond_refined_d	0.028
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3372
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
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.