Experiment: 5D40

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	25% PEG 3350, 200mM MgCl2, 100mM Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.721	α = 90
b = 99.207	β = 90
c = 105.294	γ = 90

Symmetry
Space Group	P 21 21 21

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		2015-02-13	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	72.206	97.5	0.1	0.113	0.052	8	4.7	120407	120407

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	1.51	1.59	85.4		0.601	0.601	0.338	1.1	4	15251

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	4TPN	1.51	72.206	114245	6063	97.37	0.1525	0.1492	0.16	0.2153	0.22	RANDOM	13.754

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]
0.7			0.05		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	34.051
r_sphericity_bonded	9.656
r_rigid_bond_restr	3.929
r_mcangle_it	2.133
r_angle_refined_deg	1.859
r_mcbond_it	1.794
r_mcbond_other	1.794
r_angle_other_deg	0.931
r_chiral_restr	0.145
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	34.051
r_sphericity_bonded	9.656
r_rigid_bond_restr	3.929
r_mcangle_it	2.133
r_angle_refined_deg	1.859
r_mcbond_it	1.794
r_mcbond_other	1.794
r_angle_other_deg	0.931
r_chiral_restr	0.145
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6284
Nucleic Acid Atoms
Solvent Atoms	1155
Heterogen Atoms	171

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.