9H10 | pdb_00009h10

Crystal structure of a computationally designed protein bound to a Au-containing cofactor ([(sulfaNHC)Au.TRP])

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	6.95 mgmL-1 protein (in 20 mM MES pH 5.0, 150 mM NaCl), coincubated with 2X cofactor concentration overnight at 4 C. 2% MeCN final (v/v). Incubate 0.2 uL with 0.2 uL mother liquor (50 mM HEPES pH 7.0, 12% (w/v) PEG 3350, 1% (w/v) tryptone). Crystals grow in 1-2 days

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.941	α = 90
b = 60.354	β = 93.05
c = 53.792	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	PIXEL	DECTRIS EIGER2 X 16M		2024-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97626	Diamond	I03

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	2.05	53.72	99.8	0.999	10.4	1.9		14494

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	2.05	2.11			0.778	2.3

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	2.05	40.13	14487		99.69	0.2005	0.2009	0.236	0.2423	RANDOM	35.33

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.342
r_long_range_B_refined	7.808
r_long_range_B_other	7.787
r_scangle_other	6.518
r_dihedral_angle_2_deg	5.483
r_dihedral_angle_1_deg	4.935
r_scbond_other	4.222
r_scbond_it	4.221
r_mcangle_other	3.642
r_mcangle_it	3.639
r_mcbond_it	2.527
r_mcbond_other	2.52
r_angle_refined_deg	1.588
r_angle_other_deg	0.492
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
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	1553
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	32

Software

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