9WSG | pdb_00009wsg

ToFrO 15E_to_15Z_1ns

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9WS1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293.15	5% (w/v) 1-Ethyl-3-methylimidazolium trifluoromethanesulfonate and 15% (w/v) PEG 20,000

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.04	α = 90
b = 53.87	β = 101.15
c = 79.95	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	293.15	PIXEL	CS-PAD CXI-2		2025-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.3	SLAC LCLS	CXI

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	2.6	19.82	100	0.79	4.58	134.19		12753

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	2.6	2.64			0.52

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	9WS1	2.601	18.505	12711	639	99.476	0.272	0.2718	0.2716	0.2829	0.2824	17.629

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]
0.109		-0.01	-0.295		0.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	18.346
r_dihedral_angle_6_deg	16.486
r_dihedral_angle_3_deg	14.614
r_dihedral_angle_1_deg	4.47
r_angle_other_deg	2.931
r_lrange_it	2.88
r_lrange_other	2.843
r_mcangle_it	2.372
r_mcangle_other	2.371
r_scangle_it	2.368
r_scangle_other	2.368
r_angle_refined_deg	1.703
r_scbond_it	1.689
r_scbond_other	1.688
r_mcbond_it	1.605
r_mcbond_other	1.599
r_dihedral_angle_2_deg	1.317
r_symmetry_xyhbond_nbd_refined	0.901
r_symmetry_nbd_refined	0.653
r_nbd_other	0.623
r_xyhbond_nbd_refined	0.254
r_symmetry_nbd_other	0.22
r_nbd_refined	0.19
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.105
r_chiral_restr	0.049
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2435
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
CrystFEL	data scaling
PHASER	phasing