Experiment: 6N2K

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	277	0.1M Na Citrate, pH 4.2 25% PEG 8000 0.2M Amm Acetate

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.969	α = 90
b = 49.975	β = 90
c = 92.623	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 R 1M	Osmic confocal	2016-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	1.72	30	99.5	0.051	0.08	0.04	23.5	6.05		21046

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.75	91.7		0.088	0.123	0.086	7.1	2.1

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	4LYJ	1.72	29.58	19413	936	99.82	0.1204	0.1177	0.1717	RANDOM	11.087

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]
-0.24			-0.11		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.682
r_dihedral_angle_4_deg	21.022
r_dihedral_angle_3_deg	11.845
r_dihedral_angle_1_deg	6.046
r_rigid_bond_restr	2.645
r_angle_refined_deg	1.972
r_angle_other_deg	1.531
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.682
r_dihedral_angle_4_deg	21.022
r_dihedral_angle_3_deg	11.845
r_dihedral_angle_1_deg	6.046
r_rigid_bond_restr	2.645
r_angle_refined_deg	1.972
r_angle_other_deg	1.531
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1355
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	67

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.