6ZMA

Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	294	MiaE:20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl reservoir solution: 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8 frozen under 140 bar of krypton Krypton atoms were located in anomalous map

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.622	α = 90
b = 52.3	β = 90.74
c = 79.407	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS3 S 6M		2018-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8610	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.15	80	94.6	0.076	0.99	15.7	6.1		25240		1.4	48.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.28	72.8		0.095	0.69	1.4	3.9

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	2ITB	2.15	79.4	23939	1290	94.61	0.1828	0.1796	0.2439	RANDOM	48.887

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]
-2.27		-1.51	0.92		1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.152
r_dihedral_angle_3_deg	17.038
r_dihedral_angle_4_deg	17.003
r_dihedral_angle_1_deg	5.489
r_angle_refined_deg	1.435
r_angle_other_deg	0.977
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.152
r_dihedral_angle_3_deg	17.038
r_dihedral_angle_4_deg	17.003
r_dihedral_angle_1_deg	5.489
r_angle_refined_deg	1.435
r_angle_other_deg	0.977
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3131
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	101

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	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 R01GM133198.