Experiment: 8D5E

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		309.15	15% w/v PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.75	α = 90
b = 80.59	β = 90
c = 100.02	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 24-ID-E	0.98	APS	24-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	2.46	47.391	99.9	0.19	0.208	0.084	0.988	10.7	6		16346

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	2.46	2.56	99.5		0.813	0.895	0.368	0.782		5.7

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	PDB entry 5KD7	2.46	47.391	16346	821	99.859	0.201	0.1993	0.2	0.2416	0.24	RANDOM	38.695

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]
-1.572			-0.761		2.333

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.042
r_dihedral_angle_3_deg	15.476
r_lrange_it	7.872
r_dihedral_angle_2_deg	7.771
r_dihedral_angle_1_deg	6.544
r_scangle_it	5.127
r_mcangle_it	3.714
r_scbond_it	3.224
r_mcbond_it	2.306
r_angle_refined_deg	1.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.042
r_dihedral_angle_3_deg	15.476
r_lrange_it	7.872
r_dihedral_angle_2_deg	7.771
r_dihedral_angle_1_deg	6.544
r_scangle_it	5.127
r_mcangle_it	3.714
r_scbond_it	3.224
r_mcbond_it	2.306
r_angle_refined_deg	1.417
r_nbtor_refined	0.305
r_nbd_refined	0.196
r_symmetry_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.167
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.095
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3129
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
BUCCANEER	model building
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.