6RI2 | pdb_00006ri2

Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by chloride anions at sub-atomic resolution. Twentieth structure of the series with 4065 KGy dose.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E9N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4	294	CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (12MG/ML, 20 MM K-PHOSPHATE BUFFER, PH 6.5) RESERVOIR SOLUTION (0.1 M CITRATE-PHOSPHATE BUFFER PH 4.0, 0.2 M AMMONIUM ACETATE, 25% PEG 4000). Before collecting the diffraction data, the crystal was soaked in reservoir solution containing 0.1 M NaCl.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 84.19	β = 90
c = 112.13	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 PILATUS 6M		2017-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.886	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.09	70	99.5	0.075	0.997	10.3	4.7		220475

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.09	1.12	99.9		0.853	0.734	2

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	5E9N	1.09	67.33	209495	10980	99.51	0.1293	0.12807	0.12	0.15296	0.15	RANDOM	13.868

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]
-1.7			-0.09		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.354
r_sphericity_free	24.936
r_dihedral_angle_4_deg	21.577
r_sphericity_bonded	15.056
r_dihedral_angle_3_deg	10.75
r_dihedral_angle_1_deg	6.783
r_rigid_bond_restr	5.477
r_long_range_B_refined	3.139
r_long_range_B_other	2.739
r_scangle_other	2.718
r_scbond_other	2.305
r_scbond_it	2.299
r_angle_refined_deg	1.926
r_mcangle_it	1.765
r_mcangle_other	1.76
r_mcbond_it	1.397
r_mcbond_other	1.393
r_angle_other_deg	1.097
r_chiral_restr	0.142
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3758
Nucleic Acid Atoms
Solvent Atoms	642
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing