Experiment: 6SPK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	2.6 M Ammonium sulphate, 100 mM Tris-HCl pH 7.6, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.663	α = 90
b = 195.546	β = 98.08
c = 76.34	γ = 90

Symmetry
Space Group	C 1 2 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-F		2018-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	2.77	97.77	100	0.171	0.205	0.111	0.972	4.7	3.3		41466			46.637

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	2.77	2.88	100		0.665	0.795	0.431	0.674	1.9	3.4

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	1UXM	2.77	97.08	36964	1851	93.55	0.2129	0.2112	0.21	0.2288	0.23	RANDOM	44.464

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]
-1.76		1.66	-1.66		2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.452
r_dihedral_angle_4_deg	24.467
r_dihedral_angle_3_deg	15.509
r_dihedral_angle_1_deg	12.397
r_mcangle_it	4.479
r_mcbond_it	2.632
r_mcbond_other	2.631
r_angle_other_deg	2.408
r_angle_refined_deg	1.295
r_chiral_restr	0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.452
r_dihedral_angle_4_deg	24.467
r_dihedral_angle_3_deg	15.509
r_dihedral_angle_1_deg	12.397
r_mcangle_it	4.479
r_mcbond_it	2.632
r_mcbond_other	2.631
r_angle_other_deg	2.408
r_angle_refined_deg	1.295
r_chiral_restr	0.042
r_bond_other_d	0.037
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6672
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	330

Software

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