Experiment: 4XDZ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	0.1 M bis-tris pH 6, 22% polyethylene glycol monomethylether 5000

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.579	α = 90
b = 90.753	β = 100.25
c = 69.525	γ = 90

Symmetry
Space Group	P 1 21 1

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		2014-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.15	68.415	95	0.079	0.096	0.054	6.9	3		236179

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.21	82.4		0.87	0.87	0.643	0.9	2.5	28356

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	4KQX	1.15	68.415	224341	11215	94.87	0.1582	0.1565	0.16	0.1895	0.19	RANDOM	13.086

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]
-0.23		-0.01	0.1		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	24.013
r_rigid_bond_restr	7.914
r_sphericity_bonded	7.468
r_angle_refined_deg	2.461
r_mcangle_it	1.86
r_mcbond_it	1.565
r_mcbond_other	1.561
r_angle_other_deg	1.034
r_chiral_restr	0.287
r_bond_refined_d	0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	24.013
r_rigid_bond_restr	7.914
r_sphericity_bonded	7.468
r_angle_refined_deg	2.461
r_mcangle_it	1.86
r_mcbond_it	1.565
r_mcbond_other	1.561
r_angle_other_deg	1.034
r_chiral_restr	0.287
r_bond_refined_d	0.024
r_gen_planes_refined	0.016
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5139
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	178

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
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.