8S6P | pdb_00008s6p

Crystal structure of a computationally designed protein bound to a Ru-containing cofactor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished structure of apo protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystal 1: 24% PEG 3350, 2% PEG 400, 50 mM HEPES pH 6.8, 150 mM NaCl Crystal 2: 22% PEG 8000, 100 mM Na cacodylate, 200 mM Na acetate trihydrate pH 5

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.165	α = 90
b = 85.142	β = 90
c = 90.235	γ = 90

Symmetry
Space Group	I 2 2 2

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 EIGER2 X 16M		2023-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.9	45.81	100	0.026	1	10.79	26.6		4786

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.08	100		0.797	0.807	1.3	25.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.9	45.1	4786		99.64	0.2631	0.2554	0.3184	0.2966	RANDOM	143.3

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]
-8.59			-2.83		11.42

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	27.481
r_long_range_B_other	27.48
r_scangle_other	18.298
r_mcangle_other	15.698
r_mcangle_it	15.695
r_dihedral_angle_3_deg	14.867
r_scbond_it	11.125
r_scbond_other	11.118
r_mcbond_it	10.201
r_mcbond_other	10.196
r_dihedral_angle_2_deg	6.044
r_dihedral_angle_1_deg	4.364
r_angle_refined_deg	1.676
r_angle_other_deg	0.479
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1577
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	44

Software

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