Experiment: 6AXX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XFX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	PEG3350, NaI, MIB, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.646	α = 90
b = 91.646	β = 90
c = 57.695	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CMOS	RDI CMOS_8M		2016-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.000031	ALS	4.2.2

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	2.6	45.82	99.5	0.107	0.112	0.034	0.999	18.3	10.6		8617

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	2.6	2.71	96		1.391	1.469	0.466	0.577		9.7

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	4XFX	2.6	45.8	8101	512	99.68	0.1931	0.1896	0.2	0.2465	0.25	RANDOM	69.192

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]
-0.02	-0.01		-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.979
r_sphericity_free	33.13
r_sphericity_bonded	32.167
r_dihedral_angle_4_deg	17.618
r_dihedral_angle_3_deg	13.513
r_dihedral_angle_1_deg	5.899
r_angle_refined_deg	1.315
r_angle_other_deg	0.931
r_chiral_restr	0.061
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.979
r_sphericity_free	33.13
r_sphericity_bonded	32.167
r_dihedral_angle_4_deg	17.618
r_dihedral_angle_3_deg	13.513
r_dihedral_angle_1_deg	5.899
r_angle_refined_deg	1.315
r_angle_other_deg	0.931
r_chiral_restr	0.061
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1658
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	17

Software

Software
Software Name	Purpose
Aimless	data scaling
Blu-Ice	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
PHASER	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.