3FM6 | pdb_00003fm6

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	3FKG	PDB ENTRY 3FKG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	298	9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 16% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.333	α = 90
b = 63.333	β = 90
c = 99.226	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		2002-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97992	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.13	40	99.9	0.085	0.096	13.5	4.1	145501	145501	-3	-3	11.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.13	1.16	99.8		0.13	0.156	7	3.13	145501

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	1.13	28.323	138344	138206	7291	99.9	0.1004	0.1004	0.09965	0.1	0.11482	0.12	RANDOM	10.768

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]
0.08			0.08		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.067
r_dihedral_angle_4_deg	21.501
r_dihedral_angle_3_deg	11.199
r_sphericity_free	10.29
r_dihedral_angle_1_deg	6.174
r_sphericity_bonded	4.88
r_scangle_it	3.791
r_scbond_it	2.795
r_mcangle_it	2.695
r_mcbond_it	1.963
r_rigid_bond_restr	1.824
r_mcbond_other	1.647
r_angle_refined_deg	1.409
r_angle_other_deg	0.78
r_symmetry_vdw_other	0.292
r_symmetry_vdw_refined	0.291
r_nbd_other	0.245
r_symmetry_hbond_refined	0.241
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.183
r_metal_ion_refined	0.138
r_chiral_restr	0.094
r_nbtor_other	0.093
r_symmetry_metal_ion_refined	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2354
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	67

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling