Experiment: 4Y89

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QSQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	18% PEG 8000, 0.1 M Tris, pH 8.5, 0.2M Magnesium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.623	α = 90
b = 64.886	β = 89.99
c = 103.164	γ = 90

Symmetry
Space Group	P 1 21 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		2014-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.47	103.16	98.2	0.105	28	2.9		71599

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	1.5	82.7		0.444	1.57	1.8

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	2QSQ	1.47	103.16	67967	3613	97.92	0.1455	0.1428	0.14	0.1934	0.19	RANDOM	27.343

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]
0.12		-3.82	-0.59		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.902
r_dihedral_angle_2_deg	33.542
r_sphericity_bonded	25.345
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_4_deg	7.848
r_dihedral_angle_1_deg	6.947
r_rigid_bond_restr	5.73
r_mcangle_it	3.861
r_mcbond_other	3.277
r_mcbond_it	3.276

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.902
r_dihedral_angle_2_deg	33.542
r_sphericity_bonded	25.345
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_4_deg	7.848
r_dihedral_angle_1_deg	6.947
r_rigid_bond_restr	5.73
r_mcangle_it	3.861
r_mcbond_other	3.277
r_mcbond_it	3.276
r_angle_refined_deg	1.901
r_angle_other_deg	0.994
r_chiral_restr	0.139
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3522
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
MOLREP	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.