6OO1 | pdb_00006oo1

Dehaloperoxidase B in complex with substrate o-cresol

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	6.5	277	MPEG 2000, ammonium sulphate, sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.273	α = 90
b = 67.69	β = 90
c = 67.68	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	CCD	RAYONIX MX300-HS		2019-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	1.6	37.26	98.44	0.054	0.025	0.997	28.6	3.9		34115		2	16.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.643	85.97		0.594	0.36	0.721		2

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ixf	1.602	37.26	35955	1840	98.445	0.172	0.171	0.1986	18.364

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]
1.346			-0.692		-0.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.215
r_dihedral_angle_4_deg	19.477
r_dihedral_angle_3_deg	14.331
r_dihedral_angle_1_deg	5.45
r_lrange_it	5.204
r_lrange_other	5.17
r_angle_refined_deg	1.53
r_angle_other_deg	1.502
r_scangle_it	1.144
r_scangle_other	1.126
r_mcangle_it	0.792
r_mcangle_other	0.792
r_scbond_it	0.782
r_scbond_other	0.762
r_mcbond_it	0.455
r_mcbond_other	0.453
r_nbd_refined	0.258
r_symmetry_nbd_other	0.187
r_nbd_other	0.184
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.019
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2142
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	156

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing