2GVK | pdb_00002gvk

Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	4.5	277	0.2M Li2SO4, 2.5M NaCl, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.09	α = 90
b = 109.09	β = 90
c = 122.1	γ = 120

Symmetry
Space Group	P 63 2 2

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	Flat collimating mirror, toroid focusing mirror	2006-03-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97920, 0.97903, 0.91837	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	29.05	99.7	0.097	12.9	14.16		56989			24.466

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	98.7	90.4	0.884	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	1.6	28.01	56989	2886	99.86	0.165	0.16542	0.164	0.18	0.19	0.2	RANDOM	13.932

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]
0.56	0.28		0.56		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.633
r_dihedral_angle_3_deg	12.043
r_dihedral_angle_4_deg	10.544
r_dihedral_angle_1_deg	5.99
r_scangle_it	4.138
r_scbond_it	2.634
r_mcangle_it	1.017
r_angle_refined_deg	0.957
r_angle_other_deg	0.571
r_mcbond_it	0.408
r_symmetry_vdw_refined	0.273
r_symmetry_vdw_other	0.246
r_nbd_refined	0.22
r_nbd_other	0.202
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_other	0.143
r_symmetry_hbond_refined	0.141
r_nbtor_other	0.089
r_chiral_restr	0.06
r_metal_ion_refined	0.05
r_mcbond_other	0.025
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2388
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing