7W5S | pdb_00007w5s

A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Ammonium Sulfate, HEPES pH 7.5, PEG 400, di-Potassium hydrogen phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.492	α = 90
b = 72.33	β = 90
c = 81.117	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	CMOS	BRUKER PHOTON 100		2020-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	1.76	37.63	99.8	0.053	25.5	9.4		31366

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	1.76	1.79			0.193

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	1.76	32.09	29286	1546	98.52	0.1502	0.1485	0.16	0.1815	0.19	RANDOM	14.608

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]
-5.82			-4.13		9.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.014
r_dihedral_angle_4_deg	18.33
r_dihedral_angle_3_deg	13.847
r_dihedral_angle_1_deg	6.739
r_angle_refined_deg	1.787
r_angle_other_deg	1.511
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.014
r_dihedral_angle_4_deg	18.33
r_dihedral_angle_3_deg	13.847
r_dihedral_angle_1_deg	6.739
r_angle_refined_deg	1.787
r_angle_other_deg	1.511
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2311
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
SADABS	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.