8RTO | pdb_00008rto

Bilirubin oxidase from Myrothecium verrucaria in complex with ATP

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, HANGING DROP	3.5	291.15	14% (w/v) PEG 3350, 0.1 M citric acid, pH 3.5; protein concentration 25 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.468	α = 90
b = 204.726	β = 90
c = 221.388	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MARMOSAIC 225 mm CCD		2012-05-29	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	2.4	46.95	90.4	0.122	0.139	0.065	0.992	10.5	4.2		106801		-3.7	23.6

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	2.4	2.44	93.6		0.636	0.73	0.346	0.689	2.2	4.1

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	2.4	46.499	106800	5384	89.841	0.17	0.16969	0.1701	0.1757	0.22425	0.1881	RANDOM SELECTION	28.048

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]
0.513			-0.883		0.369

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.107
r_dihedral_angle_4_deg	18.772
r_dihedral_angle_3_deg	13.903
r_dihedral_angle_1_deg	8.384
r_lrange_it	6.123
r_lrange_other	6.093
r_scangle_it	4.222
r_scangle_other	4.222
r_mcangle_it	3.591
r_mcangle_other	3.591
r_scbond_it	2.678
r_scbond_other	2.678
r_mcbond_it	2.341
r_mcbond_other	2.34
r_angle_refined_deg	1.775
r_angle_other_deg	1.252
r_nbd_other	0.237
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.197
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.169
r_metal_ion_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16962
Nucleic Acid Atoms
Solvent Atoms	1465
Heterogen Atoms	398

Software

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