Experiment: 4YY4

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	7.5	277	0.1 M HEPES, pH 7.5, 25% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.145	α = 90
b = 68.546	β = 90
c = 105.176	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	RAYONIX MX300-HS	mirrors	2012-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-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	1.47	50	96.5	0.053	10.6	5.8		21295

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	1.47	1.52	80.8		0.452		4.9	1746

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	PDB entry 3HME	1.47	32.59	20147	1087	96.26	0.2178	0.2169	0.2343	RANDOM	28.83

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]
0.33			3.48		-3.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.178
r_dihedral_angle_4_deg	26.017
r_dihedral_angle_3_deg	14.957
r_dihedral_angle_1_deg	4.664
r_scbond_it	4.153
r_mcangle_it	3.327
r_angle_refined_deg	2.764
r_mcbond_it	2.45
r_chiral_restr	0.2
r_bond_refined_d	0.032

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.178
r_dihedral_angle_4_deg	26.017
r_dihedral_angle_3_deg	14.957
r_dihedral_angle_1_deg	4.664
r_scbond_it	4.153
r_mcangle_it	3.327
r_angle_refined_deg	2.764
r_mcbond_it	2.45
r_chiral_restr	0.2
r_bond_refined_d	0.032
r_gen_planes_refined	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	825
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.