Experiment: 4YNM

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG 3350, 20 mM Tris

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.141	α = 90
b = 59.141	β = 90
c = 230.983	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	123	CCD	MARMOSAIC 300 mm CCD		2012-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97872	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.19	50	99.9	0.095	0.101	0.033	7.8	9.1		25099

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.24	100		0.59	0.626	0.204	0.865		9.1	1213

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	3OPE	2.19	46.82	23762	1271	99.86	0.2438	0.2421	0.2775	RANDOM	42.453

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]
0.08	0.04		0.08		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.596
r_dihedral_angle_4_deg	25.239
r_dihedral_angle_3_deg	18.653
r_dihedral_angle_1_deg	6.998
r_scangle_it	4.678
r_scbond_it	2.993
r_mcangle_it	2.071
r_angle_refined_deg	1.769
r_mcbond_it	1.099
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.596
r_dihedral_angle_4_deg	25.239
r_dihedral_angle_3_deg	18.653
r_dihedral_angle_1_deg	6.998
r_scangle_it	4.678
r_scbond_it	2.993
r_mcangle_it	2.071
r_angle_refined_deg	1.769
r_mcbond_it	1.099
r_chiral_restr	0.122
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3333
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	60

Software

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