Experiment: 7PSX

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	295	27% PEG 1000, 8% PEG 200, 0.15M KCl, 0.1M MgCl2, 0.05M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.64	57.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.153	α = 88.02
b = 55.541	β = 81.46
c = 101.08	γ = 84.94

Symmetry
Space Group	P 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		2018-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

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	1.97	48.85	97.2	0.284	0.326	0.158	0.97	2.4	4		55783

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	1.97	2.02	77.7		5.776	6.922	3.728	0.074		3.2

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	5EDN	2	47	52887	1603	98.64	0.2608	0.2601	0.28	0.2831	0.3	RANDOM	40.422

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]
1.88	-0.63	2.26	-1.05	-0.69	-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.706
r_dihedral_angle_4_deg	19.023
r_dihedral_angle_3_deg	19.011
r_dihedral_angle_1_deg	5.191
r_angle_refined_deg	1.484
r_angle_other_deg	1.448
r_chiral_restr	0.076
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.706
r_dihedral_angle_4_deg	19.023
r_dihedral_angle_3_deg	19.011
r_dihedral_angle_1_deg	5.191
r_angle_refined_deg	1.484
r_angle_other_deg	1.448
r_chiral_restr	0.076
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2039
Nucleic Acid Atoms	2968
Solvent Atoms	356
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

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.