7QWI | pdb_00007qwi

Vanadate complex of the vanadium-dependent bromoperoxidase from Corallina pilulifera

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UP8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	50 mM Tris-H2SO4, pH 6.8, 0.4M KBr, 1mM Na3VO4, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.601	α = 90
b = 199.601	β = 90
c = 199.601	γ = 90

Symmetry
Space Group	P 21 3

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		2003-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9200	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	2.15	14.965	96.4	0.155	0.977	8.1	4.9		142571

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19			0.502	0.809

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1up8	2.15	14.965	141462	7104	98.889	0.147	0.1443	0.14	0.1945	0.19	19.248

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.498
r_dihedral_angle_4_deg	17.836
r_dihedral_angle_3_deg	13.457
r_lrange_it	6.985
r_scangle_it	6.469
r_dihedral_angle_1_deg	6.081
r_scbond_it	5.582
r_mcangle_it	3.809
r_mcbond_it	3.248
r_angle_refined_deg	1.333
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.143
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.091
r_metal_ion_refined	0.085
r_ncsr_local_group_1	0.054
r_ncsr_local_group_4	0.053
r_ncsr_local_group_3	0.052
r_ncsr_local_group_6	0.052
r_ncsr_local_group_5	0.05
r_ncsr_local_group_2	0.044
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18448
Nucleic Acid Atoms
Solvent Atoms	2952
Heterogen Atoms	365

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
O	model building
Coot	model building