Experiment: 8D5F

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5KD7	{DB entry 5KD7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	309.15	20% PEG3350, 200 nM sodium tartrate dibasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.3	α = 90
b = 68.86	β = 90
c = 109.44	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 EIGER X 16M		2019-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-E	0.98	APS	21-ID-E

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	2.31	47.233	99.2	0.12	0.143	0.077	0.993	10.7	6		17756			29.8

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	2.31	2.39			0.046	0.054	0.027	0.996		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 (All)	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	{DB entry 5KD7	2.31	47.233	17755	891	98.875	0.193	0.193	0.19	0.1991	0.19	RANDOM	35.928

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]
-0.492			0.358		0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.552
r_dihedral_angle_3_deg	18.254
r_dihedral_angle_1_deg	7.3
r_lrange_it	7.202
r_scangle_it	4.14
r_mcangle_it	2.937
r_scbond_it	2.508
r_dihedral_angle_2_deg	2.091
r_angle_refined_deg	1.979
r_mcbond_it	1.718

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.552
r_dihedral_angle_3_deg	18.254
r_dihedral_angle_1_deg	7.3
r_lrange_it	7.202
r_scangle_it	4.14
r_mcangle_it	2.937
r_scbond_it	2.508
r_dihedral_angle_2_deg	2.091
r_angle_refined_deg	1.979
r_mcbond_it	1.718
r_nbtor_refined	0.309
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.182
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.126
r_bond_refined_d	0.011
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3134
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	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.