Experiment: 4YPA

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	PEG 4000, magnesium chloride, Tris

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.682	α = 91.57
b = 61.773	β = 93.83
c = 73.233	γ = 90.46

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		2014-08-22	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	2.3	50	96	0.06	8.1	2		40091

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	2.3	2.34	97.3		0.255		2	2023

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	4YNM	2.3	73.04	38087	2003	95.7	0.2517	0.2489	0.303	RANDOM	38.039

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]
0.07	-0.15	-0.15	0.16	-0.09	-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.506
r_dihedral_angle_3_deg	18.956
r_dihedral_angle_4_deg	18.546
r_dihedral_angle_1_deg	6.788
r_scangle_it	4.041
r_scbond_it	2.538
r_mcangle_it	1.836
r_angle_refined_deg	1.644
r_mcbond_it	0.987
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.506
r_dihedral_angle_3_deg	18.956
r_dihedral_angle_4_deg	18.546
r_dihedral_angle_1_deg	6.788
r_scangle_it	4.041
r_scbond_it	2.538
r_mcangle_it	1.836
r_angle_refined_deg	1.644
r_mcbond_it	0.987
r_chiral_restr	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6920
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
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 R01GM133198.