3FKG | pdb_00003fkg

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QPA	PDB ENTRY 1QPA

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, 17% PEG 10000, 200mM Zn-acetate, 100mM Na-cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.683	α = 90
b = 62.683	β = 90
c = 98.217	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	MARMOSAIC 325 mm CCD		2001-11-14	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	1.81	40	96.1	0.056	11.9	2.4	34670	33318	1	1	20.3

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	1.81	1.84	98.6		0.392	1.1

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 1QPA	1.81	32.9	31531	31531	1667	96.11	0.15465	0.15217	0.15	0.201	0.2	RANDOM	25.889

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]
-0.04			-0.04		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.504
r_dihedral_angle_4_deg	21.18
r_dihedral_angle_3_deg	13.652
r_dihedral_angle_1_deg	7.302
r_scangle_it	4.354
r_mcangle_it	3.344
r_scbond_it	3.188
r_mcbond_it	2.509
r_angle_refined_deg	1.442
r_symmetry_hbond_refined	0.434
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.21
r_chiral_restr	0.116
r_metal_ion_refined	0.112
r_symmetry_metal_ion_refined	0.049
r_gen_planes_refined	0.017
r_bond_refined_d	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2360
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	65

Software

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