9G7Q | pdb_00009g7q

Structure of the StayRose dimer

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BXT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	Structure Screen condition E9 Ethylene glycol as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.306	α = 90
b = 133.306	β = 90
c = 58.35	γ = 120

Symmetry
Space Group	P 61

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		2022-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

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	1.65	43.63	98.5	0.15	0.033	0.999	14.3	20.7		70220			15.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	95.4		1.423	0.335	0.784	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.65	43.63	70210	3503	98.484	0.156	0.1544	0.1671	0.1785	0.1888	COPIED FROM 8BXT	18.368

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]
0.393	0.196		0.393		-1.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.803
r_dihedral_angle_2_deg	14.578
r_dihedral_angle_other_2_deg	14.155
r_dihedral_angle_3_deg	11.762
r_dihedral_angle_1_deg	7.382
r_lrange_it	6.069
r_lrange_other	5.949
r_scangle_it	4.918
r_scangle_other	4.917
r_scbond_it	3.229
r_scbond_other	3.228
r_mcangle_it	2.7
r_mcangle_other	2.7
r_mcbond_it	1.83
r_mcbond_other	1.83
r_angle_refined_deg	1.808
r_angle_other_deg	0.644
r_nbd_other	0.24
r_symmetry_nbd_other	0.204
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.095
r_symmetry_xyhbond_nbd_other	0.029
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3459
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing