6US6

Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QCB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	295	26 mg/mL protein, 2.0 M ammonium sulfate, 0.1 M sodium acetate pH 4

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.117	α = 90
b = 58.117	β = 90
c = 185.667	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	CCD	RAYONIX MX340-HS		2018-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.3017	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1	6011

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	1.5	23.22	99.8	0.977	27.544	99.98		26030

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	1.5	1.55	99.5		0.24	0.967	13.24

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QCB	1.5	23.22	24705	1325	99.75	0.1682	0.1674	0.1821	RANDOM	21.843

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.041
r_dihedral_angle_4_deg	23.856
r_dihedral_angle_3_deg	14.677
r_dihedral_angle_1_deg	7.345
r_angle_other_deg	2.543
r_angle_refined_deg	1.996
r_chiral_restr	0.089
r_bond_other_d	0.038
r_gen_planes_other	0.022
r_bond_refined_d	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.041
r_dihedral_angle_4_deg	23.856
r_dihedral_angle_3_deg	14.677
r_dihedral_angle_1_deg	7.345
r_angle_other_deg	2.543
r_angle_refined_deg	1.996
r_chiral_restr	0.089
r_bond_other_d	0.038
r_gen_planes_other	0.022
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	935
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
DIALS	data scaling
PHASER	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.