Experiment: 5YS9

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	Pentaerythritol propoxylate, KCl, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.824	α = 90
b = 160.824	β = 90
c = 139.467	γ = 90

Symmetry
Space Group	I 4

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	ADSC QUANTUM 270	Rh coated Torroidal Mirror	2015-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	2.5	50	98.8	0.07	0.076	0.03	20.5	5.5		60127

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	2.5	2.54	98		0.281	0.318	0.145	0.889		4.3

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	pdbid 5Y9D	2.5	35.99	57083	3044	98.62	0.1829	0.1807	0.2293	RANDOM	45.449

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]
-0.17			-0.17		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.783
r_dihedral_angle_4_deg	22.714
r_dihedral_angle_3_deg	18.969
r_dihedral_angle_1_deg	6.268
r_angle_refined_deg	1.677
r_angle_other_deg	0.883
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.783
r_dihedral_angle_4_deg	22.714
r_dihedral_angle_3_deg	18.969
r_dihedral_angle_1_deg	6.268
r_angle_refined_deg	1.677
r_angle_other_deg	0.883
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10855
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	106

Software

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

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.