9DJS | pdb_00009djs

T4 Lysozyme A73H/G77H/T115H/R119H co-crystallized with Cu(II)-NTA (room temperature structure)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	102L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	293	Protein: 0.33 mM T4 lysozyme mutant, 4.95 mM Cu(II)-NTA. Precipitant: 2.2 M NaH2PO4/K2HPO4, pH 6.6, 150 mM NaCl, 100 mM 1,6-hexanediol, 3% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.721	α = 90
b = 60.721	β = 90
c = 97.311	γ = 120

Symmetry
Space Group	P 32 2 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	DECTRIS EIGER R 1M		2024-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU MICROMAX-003	1.5418

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	1.55	27.61	98	0.995	10.81	4.4		30207			18.98

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	1.55	1.61	94.4		0.488	1.28	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.55	27.61	1.33	29671	1964	96.43	0.1769	0.1754	0.1748	0.1968	0.1968	24.01

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
f_dihedral_angle_d	22.1006
f_angle_d	1.3999
f_chiral_restr	0.0886
f_bond_d	0.0152
f_plane_restr	0.0095

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1305
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	33

Software

Software
Software Name	Purpose
PHENIX	refinement
CrysalisPro	data collection
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.