7QYY | pdb_00007qyy

Vanadium-dependent bromoperoxidase from Corallina pilulifera in complex with chloride

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		291	0.1M Tris-HBr, pH 7.4, 1.3M ammonium dihydrogen phosphate

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.115	α = 90
b = 182.115	β = 90
c = 177.602	γ = 120

Symmetry
Space Group	P 63

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		2002-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.84820	EMBL/DESY, HAMBURG	BW7A

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	1.999	99	97.4	0.063	11.2	3.3		218890

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	1.999	2.07			0.219	2.7

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	1.999	19.962	211873	10625	94.254	0.148	0.146	0.15	0.1928	0.19	24.081

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]
0.283	0.141		0.283		-0.918

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.345
r_dihedral_angle_4_deg	17.029
r_dihedral_angle_3_deg	13.298
r_scangle_it	9.257
r_lrange_it	9.081
r_scbond_it	8.651
r_dihedral_angle_1_deg	6.193
r_mcangle_it	5.558
r_mcbond_it	5.313
r_angle_refined_deg	1.772
r_nbtor_refined	0.323
r_metal_ion_refined	0.29
r_symmetry_nbd_refined	0.237
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.118
r_ncsr_local_group_4	0.055
r_ncsr_local_group_2	0.054
r_ncsr_local_group_6	0.054
r_ncsr_local_group_1	0.053
r_ncsr_local_group_3	0.049
r_ncsr_local_group_5	0.049
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18420
Nucleic Acid Atoms
Solvent Atoms	3214
Heterogen Atoms	460

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing