8B74 | pdb_00008b74

Tyrosinase from halophilic bacterium Hahella sp. CCB MM4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	300	0.2 M LiSO4, 0.1 Bis-Tris pH 5.5, 20 % (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.14	α = 90
b = 55.572	β = 90
c = 156.298	γ = 90

Symmetry
Space Group	P 2 2 21

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 9M		2022-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.97625	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.965	78.271	99.2	0.081	0.997	9.7	3.7		32382

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.965	1.999	100		0.565	0.781		3.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Alphafold	1.965	78.271	32381	1557	99.164	0.177	0.1748	0.19	0.2262	0.23	32.633

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]
2.961			-1.926		-1.035

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.102
r_dihedral_angle_6_deg	16.539
r_dihedral_angle_2_deg	10.55
r_lrange_other	9.337
r_lrange_it	9.322
r_scangle_it	8.082
r_scangle_other	8.081
r_dihedral_angle_1_deg	8.049
r_scbond_it	6.438
r_scbond_other	6.437
r_mcangle_other	5.354
r_mcangle_it	5.348
r_mcbond_other	4.136
r_mcbond_it	4.133
r_angle_refined_deg	2.111
r_angle_other_deg	0.735
r_nbd_other	0.316
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.233
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_refined	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3408
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms

Software

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