Experiment: 8OQK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X7F	1X7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Sodium cacodylate, MPD, PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.94	α = 90
b = 131.94	β = 90
c = 89.22	γ = 90

Symmetry
Space Group	I 41 2 2

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 2M-F		2018-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	49.216	100	0.999	19.58	26.63		26844

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.534

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1X7F	2	49.216	26843	1343	99.985	0.179	0.1771	0.18	0.2057	0.21	41.513

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]
-0.277			-0.277		0.555

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.699
r_dihedral_angle_6_deg	15.457
r_dihedral_angle_3_deg	14.512
r_lrange_it	8.264
r_scangle_it	6.887
r_dihedral_angle_1_deg	6.335
r_scbond_it	5.735
r_mcangle_it	4.031
r_mcbond_it	3.594
r_angle_refined_deg	1.464

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.699
r_dihedral_angle_6_deg	15.457
r_dihedral_angle_3_deg	14.512
r_lrange_it	8.264
r_scangle_it	6.887
r_dihedral_angle_1_deg	6.335
r_scbond_it	5.735
r_mcangle_it	4.031
r_mcbond_it	3.594
r_angle_refined_deg	1.464
r_nbtor_refined	0.315
r_nbd_refined	0.207
r_symmetry_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.137
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.09
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2183
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.