Experiment: 8EDH

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	0.1M Sodium Malonate pH 5.0 and 12% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.78	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.976	α = 90
b = 112.473	β = 100.268
c = 66.642	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2019-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97925	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3.11	27.8	86	0.07	0.04	0.95	8.4	4.8		13357			44.4

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	3.11	4.8	98.4		0.4		4.9

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	FREE R-VALUE	5FPQ	3.111	26.485	10857	1046	81.301	0.196	0.1857	0.19	0.2911	0.29	10%	69.718

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]
0.239		0.213	-1.259		0.884

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	21.829
r_lrange_it	19.552
r_dihedral_angle_2_deg	15.511
r_dihedral_angle_6_deg	14.77
r_scangle_it	10.264
r_mcangle_it	9.45
r_dihedral_angle_1_deg	6.757
r_scbond_it	6.447
r_mcbond_it	5.67
r_angle_refined_deg	1.391

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4126
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.