Experiment: 4Y5R

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	292	25-30% PEG 8000, 0,1 M sodium Acetate, 0.1 M MES pH 6.4

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.53	α = 109.94
b = 83.52	β = 91.54
c = 107.78	γ = 105.78

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	IMAGE PLATE	MAR scanner 300 mm plate		2014-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.003	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.58	29.61	95.2	0.111	0.111	0.902	5.2	1.9		51683

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.58	2.66	66		0.639	0.639	0.437	1.2	1.8	3115

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	FOURIER SYNTHESIS	THROUGHOUT	3L4M	2.8	29.61	39834	2135	98.18	0.1964	0.1932	0.2564	RANDOM	51.054

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]
-0.93	-0.27	0.9	0.51	0.68	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.965
r_dihedral_angle_4_deg	17.947
r_dihedral_angle_3_deg	15.515
r_dihedral_angle_1_deg	6.724
r_angle_other_deg	3.712
r_angle_refined_deg	1.707
r_chiral_restr	0.079
r_gen_planes_other	0.013
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.965
r_dihedral_angle_4_deg	17.947
r_dihedral_angle_3_deg	15.515
r_dihedral_angle_1_deg	6.724
r_angle_other_deg	3.712
r_angle_refined_deg	1.707
r_chiral_restr	0.079
r_gen_planes_other	0.013
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13227
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	174

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.