6RI4 | pdb_00006ri4

Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. First structure of the series with 13 KGy dose.

X-RAY DIFFRACTION

---

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 NaF.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.14	α = 90
b = 84.17	β = 90
c = 112.18	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	1.08	70	98.6	0.0108	0.996	7.6	4.7		223934

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	1.08	1.11	99.6		0.756	0.724	1.8

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	1.08	67.33	212904	11030	98.6	0.13059	0.12952	0.13	0.15166	0.15	RANDOM	12.291

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]
-0.67			-0.8		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.985
r_dihedral_angle_4_deg	22.599
r_sphericity_free	19.718
r_sphericity_bonded	11.384
r_dihedral_angle_3_deg	11.162
r_dihedral_angle_1_deg	7.112
r_rigid_bond_restr	3.734
r_long_range_B_refined	2.68
r_long_range_B_other	2.213
r_scangle_other	2.092
r_angle_refined_deg	1.854
r_scbond_it	1.724
r_scbond_other	1.72
r_mcangle_other	1.477
r_mcangle_it	1.472
r_mcbond_other	1.331
r_mcbond_it	1.311
r_angle_other_deg	1.044
r_chiral_restr	0.133
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
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	3765
Nucleic Acid Atoms
Solvent Atoms	908
Heterogen Atoms	74

Software

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