Experiment: 8AIP

Crystal Structure of Two-domain bacterial laccase from the actinobacterium Streptomyces carpinensis VKM Ac-1300

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GYB	4GYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		297	20%v/v PEG Smear Broad, 0.1 M Sodium citratate, pH 5.6, 0.15 M Mg acetate (condition #33 of BCS-1 from Molecular Dimensions, UK)

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.962	α = 90
b = 97.962	β = 90
c = 97.962	γ = 90

Symmetry
Space Group	P 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	Bruker Platinum 135		2020-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.54178

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	2.3	33	97	0.075	0.99	6.8	4.29		13826			30.39

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	2.3	2.38	82.3		0.355	0.8	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4GYB	2.35	32.65	1.33	13065	642	97.99	0.2337	0.2312	0.2343	0.2814	0.2825	30.3

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.3493
f_angle_d	0.9574
f_chiral_restr	0.0616
f_plane_restr	0.0089
f_bond_d	0.0087

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2122
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing