Experiment: 6QYB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EI0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1.5 M Ammonium sulfate, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.276	α = 90
b = 62.202	β = 90
c = 65.169	γ = 90

Symmetry
Space Group	P 21 21 2

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 6M-F		2017-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.18	65.28	98.1	0.056	0.061	0.023	0.998	17.6	6.3		86182

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	1.18	1.2	81.6		0.809	0.951	0.491	0.61	1.2	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6EI0	1.18	65.25	81782	4301	98.01	0.1827	0.1821	0.19	0.194	0.2	RANDOM	20.41

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]
3.02			-3.89		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.25
r_dihedral_angle_4_deg	20.603
r_dihedral_angle_3_deg	15.483
r_rigid_bond_restr	4.635
r_dihedral_angle_1_deg	3.927
r_angle_other_deg	1.603
r_angle_refined_deg	1.399
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.25
r_dihedral_angle_4_deg	20.603
r_dihedral_angle_3_deg	15.483
r_rigid_bond_restr	4.635
r_dihedral_angle_1_deg	3.927
r_angle_other_deg	1.603
r_angle_refined_deg	1.399
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1696
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	39

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
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 R01GM157729.