8RTQ | pdb_00008rtq

Bilirubin oxidase from Myrothecium verrucaria with G395T mutation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I3J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	291.15	20% (w/v) PEG 3350, 0.1 M succinic acid pH 3.5, protein concentration 10 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.215	α = 90
b = 200.681	β = 90
c = 216.615	γ = 90

Symmetry
Space Group	F 2 2 2

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		2022-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	2.1	47.66	95.6	0.191	0.222	0.11	0.985	6.5	3.7		81954		-3.7	17.4

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	2.1	2.14	97.7		0.857	0.996	0.496	0.586	1.6	3.7

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 (All)	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	2.1	47.66	81954	4026	95.333	0.154	0.154	0.153	0.1619	0.197	0.1721	RANDOM SELECTION	21.047

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]
0.112			-0.582		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.117
r_dihedral_angle_4_deg	19.093
r_dihedral_angle_3_deg	13.02
r_dihedral_angle_1_deg	7.802
r_lrange_it	4.973
r_lrange_other	4.724
r_scangle_it	3.465
r_scangle_other	3.464
r_scbond_it	2.205
r_scbond_other	2.205
r_mcangle_it	2.159
r_mcangle_other	2.159
r_angle_refined_deg	1.633
r_mcbond_it	1.42
r_mcbond_other	1.417
r_angle_other_deg	1.316
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.201
r_symmetry_nbd_other	0.187
r_nbd_other	0.181
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_other	0.13
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8494
Nucleic Acid Atoms
Solvent Atoms	1139
Heterogen Atoms	269

Software

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