Experiment: 6SD0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DP0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	12% PEG 3350, 0.1 M Bis-Tris propane pH 8.5, 0.2 M NaNO3, 2% MPD, 8 mM n-Nonyl-b-D-thiomaltoside. The crystals were enhanced by the microseeding technique.

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.852	α = 90
b = 167.852	β = 90
c = 519.99	γ = 90

Symmetry
Space Group	I 4

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	KB focusing mirrors	2014-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979470	ALBA	XALOC

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	3.7	40	99.8	0.165	0.182	0.075	0.996	10.1	5.8	442617	76050

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	3.7	3.78	99.9		1.74	1.906	0.771	0.581		6

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	1DP0	3.7	40	72328	3720	99.78	0.2432	0.2411	0.24	0.2855	0.28	RANDOM	146.58

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]
38.67			38.67		-77.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.051
r_dihedral_angle_4_deg	15.251
r_dihedral_angle_3_deg	13.934
r_dihedral_angle_1_deg	7.269
r_angle_refined_deg	1.444
r_angle_other_deg	1.124
r_chiral_restr	0.057
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.051
r_dihedral_angle_4_deg	15.251
r_dihedral_angle_3_deg	13.934
r_dihedral_angle_1_deg	7.269
r_angle_refined_deg	1.444
r_angle_other_deg	1.124
r_chiral_restr	0.057
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36112
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	4

Software

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