9RCJ | pdb_00009rcj

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 20 seconds

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XJ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294	85% 1 M Ammonium Sulfate, 0.1 M Sodium Acetate pH 4.6 and 15% of another condition with 0.2 Sodium Chloride, 0.1 M Phosphate-citrate pH 4.2 and 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.396	α = 90
b = 123.396	β = 90
c = 180.345	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	180	PIXEL	DECTRIS EIGER X 16M		2024-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.37729	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	2.45	52.45	100	0.196	0.201	0.045	0.998	13.4	19.5		59007

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	2.45	2.52		100	1.977	2.031	0.463	0.824		18.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.45	52.39	55968	2982	99.97	0.19237	0.19033	0.199	0.23114	0.2339	RANDOM	42.498

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]
0.75	0.38		0.75		-2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.431
r_dihedral_angle_2_deg	7.418
r_dihedral_angle_1_deg	7.222
r_long_range_B_refined	6.81
r_long_range_B_other	6.81
r_scangle_other	4.646
r_mcangle_other	3.702
r_mcangle_it	3.701
r_scbond_it	2.865
r_scbond_other	2.861
r_mcbond_it	2.404
r_mcbond_other	2.403
r_angle_refined_deg	1.216
r_angle_other_deg	0.461
r_chiral_restr	0.064
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7293
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	23

Software

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