6SEU | pdb_00006seu

X-ray structure of the gold/lysozyme adduct formed upon 21h exposure of protein crystals to compound 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	20% ethylene glycol 0.1 M sodium acetate pH 4.5 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.953	α = 90
b = 76.953	β = 90
c = 38.889	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	RIGAKU SATURN 944		2019-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.95	34.73	99.8	0.141	0.06	0.805	13.8	13.8		8955

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	99.8		0.546	0.361	0.951	1.5	3.1

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	193L	1.95	34.73	8452	466	99.62	0.1958	0.192	0.2003	0.2603	0.2659	RANDOM	22.647

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]
-0.32			-0.32		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.391
r_dihedral_angle_4_deg	17.3
r_dihedral_angle_3_deg	13.03
r_dihedral_angle_1_deg	7.174
r_angle_refined_deg	1.525
r_angle_other_deg	1.444
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1000
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing