Experiment: 6YJ3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	290	50 MM TRIS-HCL, 1.6 M SODIUM CITRATE

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.479	α = 90
b = 100.479	β = 90
c = 42.468	γ = 120

Symmetry
Space Group	P 63

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 PILATUS 300K	Osmic VariMax ARC)SEC	2015-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.55	87.02	90.2	0.029	0.031	1	36.32	5.984		32294			19.102

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	24.8		0.228	0.29	0.901	3.39	1.12

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	6T7U	1.55	87.02	31156	1136	90.23	0.1343	0.1335	0.1545	RANDOM	14.681

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]
-0.18	-0.09		-0.18		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.135
r_dihedral_angle_4_deg	14.725
r_dihedral_angle_3_deg	11.852
r_dihedral_angle_1_deg	6.43
r_angle_other_deg	3.676
r_angle_refined_deg	1.535
r_chiral_restr	0.09
r_bond_other_d	0.021
r_bond_refined_d	0.012
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.135
r_dihedral_angle_4_deg	14.725
r_dihedral_angle_3_deg	11.852
r_dihedral_angle_1_deg	6.43
r_angle_other_deg	3.676
r_angle_refined_deg	1.535
r_chiral_restr	0.09
r_bond_other_d	0.021
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2047
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
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.