3FMU | pdb_00003fmu

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	5	298	9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 14% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.199	α = 90
b = 63.199	β = 90
c = 99.237	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		2003-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.891976	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	1.03	80	97.6	0.108	0.097	11.95	3.98	191427	186809	-3	-3	11.4

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	1.03	1.15	91.8		0.299	0.254	4.57	3.6	53827

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	1.04	44.688	176589	175971	9281	99.65	0.1151	0.11151	0.11092	0.11	0.12301	0.12	RANDOM	12.107

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		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.517
r_dihedral_angle_4_deg	19.816
r_dihedral_angle_3_deg	11.481
r_sphericity_free	10.469
r_dihedral_angle_1_deg	6.02
r_sphericity_bonded	5.034
r_scangle_it	4.054
r_scbond_it	3.051
r_mcangle_it	2.894
r_mcbond_it	2.106
r_rigid_bond_restr	1.915
r_mcbond_other	1.585
r_angle_refined_deg	1.469
r_angle_other_deg	0.773
r_symmetry_vdw_other	0.307
r_nbd_refined	0.234
r_nbd_other	0.222
r_nbtor_refined	0.184
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.152
r_chiral_restr	0.098
r_nbtor_other	0.092
r_symmetry_metal_ion_refined	0.073
r_metal_ion_refined	0.063
r_bond_refined_d	0.012
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	2348
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	63

Software

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