4MIF | pdb_00004mif

Pyranose 2-oxidase from Phanerochaete chrysosporium, wild type from natural source

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PL8	pdb entry 3PL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	298	0.1 M MES, 0.2 M MgCl2, 32% (w/v) PEG 400, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.034	α = 90
b = 164.034	β = 90
c = 232.521	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	100	CCD	MARMOSAIC 225 mm CCD	mirrors	2008-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	47.43	99.9	17.1	11.1	331914	331914

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	99.9		2.1	11.2	49157

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	pdb entry 3PL8	1.8	46.4	329915	329915	1999	99.9	0.15273	0.15261	0.16	0.171	0.18	RANDOM	29.711

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]
-0.07	-0.04		-0.07		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_4_deg	19.56
r_dihedral_angle_3_deg	13.471
r_dihedral_angle_1_deg	6.719
r_angle_refined_deg	2.226
r_angle_other_deg	1.115
r_chiral_restr	0.212
r_bond_refined_d	0.025
r_gen_planes_refined	0.013
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_4_deg	19.56
r_dihedral_angle_3_deg	13.471
r_dihedral_angle_1_deg	6.719
r_angle_refined_deg	2.226
r_angle_other_deg	1.115
r_chiral_restr	0.212
r_bond_refined_d	0.025
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18148
Nucleic Acid Atoms
Solvent Atoms	1562
Heterogen Atoms	213

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.