6Z0J | pdb_00006z0j

Crystal structure of laccase from Pediococcus acidilactici Pa5930 (Tris-HCl pH 8.5)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZDW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	30% PEG1000 and 0.1M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.797	α = 90
b = 94.294	β = 90
c = 97.564	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 S 6M		2018-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97925	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.5	94.29	100	0.148	0.16	0.058	0.995	7.9	7.3		17180

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	100		0.904	0.97	0.35	0.758		7.5

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	3ZDW	2.5	67.8	16257	865	99.94	0.2227	0.2201	0.22	0.2679	0.27	RANDOM	48.517

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]
-4.31			-2.64		6.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.279
r_dihedral_angle_3_deg	16.964
r_dihedral_angle_4_deg	15.798
r_dihedral_angle_1_deg	7.175
r_angle_refined_deg	1.264
r_angle_other_deg	1.095
r_chiral_restr	0.044
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.279
r_dihedral_angle_3_deg	16.964
r_dihedral_angle_4_deg	15.798
r_dihedral_angle_1_deg	7.175
r_angle_refined_deg	1.264
r_angle_other_deg	1.095
r_chiral_restr	0.044
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3697
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	4

Software

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

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.