Experiment: 4YYG

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	0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.117	α = 90
b = 69.825	β = 90
c = 104.554	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		2013-02-24	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	2	50	95.2	0.091	8	4.3		8638

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	2.07	83.5		0.632		4	747

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	2.1	33.12	7156	346	95.8	0.2557	0.253	0.24	0.3115	0.29	RANDOM	35.98

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]
3.42			-5.07		1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.947
r_dihedral_angle_3_deg	18.897
r_dihedral_angle_4_deg	11.999
r_dihedral_angle_1_deg	4.971
r_scbond_it	3.525
r_mcangle_it	3.36
r_mcbond_it	2.639
r_angle_refined_deg	1.967
r_chiral_restr	0.132
r_bond_refined_d	0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.947
r_dihedral_angle_3_deg	18.897
r_dihedral_angle_4_deg	11.999
r_dihedral_angle_1_deg	4.971
r_scbond_it	3.525
r_mcangle_it	3.36
r_mcbond_it	2.639
r_angle_refined_deg	1.967
r_chiral_restr	0.132
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	815
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	22

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.