3FM4 | pdb_00003fm4

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FKG	PDB ENTRY 3FKG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 16% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.794	α = 90
b = 62.794	β = 90
c = 97.875	γ = 90

Symmetry
Space Group	P 43

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	MAR CCD 165 mm		2001-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8065	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.11	40	97.6	0.084	9.1	2.8	22013	21485

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.15	78.5		0.367	1.7		839

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 (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	PDB ENTRY 3FKG	2.11	32.88	20724	20357	1095	98.23	0.14418	0.14418	0.14126	0.14	0.19776	0.2	RANDOM	28.046

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]
-0.24			-0.24		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.293
r_dihedral_angle_4_deg	16.297
r_dihedral_angle_3_deg	14.281
r_dihedral_angle_1_deg	7.412
r_scangle_it	3.998
r_mcangle_it	3.341
r_scbond_it	3.275
r_mcbond_it	2.448
r_angle_refined_deg	1.379
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.293
r_dihedral_angle_4_deg	16.297
r_dihedral_angle_3_deg	14.281
r_dihedral_angle_1_deg	7.412
r_scangle_it	3.998
r_mcangle_it	3.341
r_scbond_it	3.275
r_mcbond_it	2.448
r_angle_refined_deg	1.379
r_nbtor_refined	0.317
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.227
r_xyhbond_nbd_refined	0.204
r_symmetry_vdw_refined	0.201
r_metal_ion_refined	0.149
r_chiral_restr	0.106
r_gen_planes_refined	0.015
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2353
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	63

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.