8VQS | pdb_00008vqs

Crystal structure of Dehaloperoxidase B in complex with substrate cyclohexene

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	MPEG 2000, ammonium sulfate, sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.092	α = 90
b = 67.684	β = 90
c = 67.684	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER R 4M		2023-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	17.34	99.47	0.999	16	6.2		18829

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.051			0.705

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	17.339	18829	929	99.466	0.198	0.1946	0.203	0.251	0.2603	38.438

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]
1.496			-1.135		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.296
r_dihedral_angle_6_deg	14.569
r_lrange_it	8.549
r_lrange_other	8.525
r_dihedral_angle_2_deg	6.995
r_scangle_it	6.422
r_scangle_other	6.414
r_dihedral_angle_1_deg	6.22
r_mcangle_it	4.624
r_mcangle_other	4.623
r_scbond_it	4.434
r_scbond_other	4.411
r_mcbond_it	3.284
r_mcbond_other	3.284
r_angle_refined_deg	1.553
r_angle_other_deg	0.549
r_nbd_refined	0.268
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.188
r_xyhbond_nbd_refined	0.184
r_nbd_other	0.177
r_symmetry_nbd_refined	0.15
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2162
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing