6UIY | pdb_00006uiy

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
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.74	α = 90
b = 57.74	β = 90
c = 184.27	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	100	CCD	ADSC QUANTUM 315r		2018-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.00	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.47	55.1	100	0.069	0.072	0.02	0.999	21.6	12.9		27259

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.47	1.49	100		0.501	0.529	0.17	0.928		9.6

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QCB	1.47	55.1	25837	1383	99.94	0.154	0.1528	0.1768	RANDOM	17.436

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]
0.04			0.04		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.298
r_dihedral_angle_4_deg	15.426
r_dihedral_angle_3_deg	14.08
r_dihedral_angle_1_deg	6.976
r_angle_other_deg	3.725
r_angle_refined_deg	2.434
r_chiral_restr	0.134
r_bond_other_d	0.038
r_bond_refined_d	0.018
r_gen_planes_other	0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.298
r_dihedral_angle_4_deg	15.426
r_dihedral_angle_3_deg	14.08
r_dihedral_angle_1_deg	6.976
r_angle_other_deg	3.725
r_angle_refined_deg	2.434
r_chiral_restr	0.134
r_bond_other_d	0.038
r_bond_refined_d	0.018
r_gen_planes_other	0.017
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	935
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	75

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
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.