Experiment: 6AXY

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.915	α = 90
b = 91.915	β = 90
c = 57.919	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	2.78	45.96	97.3	0.109	0.115	0.035	0.999	18	10.6		6969

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	2.78	2.93	97.3		1.05	1.106	0.345	0.754		9.9

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 4XFX	2.78	45.96	6576	383	97.14	0.2156	0.2131	0.26	RANDOM	74.506

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]
-0.39	-0.19		-0.39		1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.873
r_dihedral_angle_4_deg	18.695
r_dihedral_angle_3_deg	12.558
r_dihedral_angle_1_deg	5.467
r_angle_refined_deg	1.085
r_angle_other_deg	0.852
r_chiral_restr	0.054
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.873
r_dihedral_angle_4_deg	18.695
r_dihedral_angle_3_deg	12.558
r_dihedral_angle_1_deg	5.467
r_angle_refined_deg	1.085
r_angle_other_deg	0.852
r_chiral_restr	0.054
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1680
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	16

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.