6HTW | pdb_00006htw

Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 184)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EFC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	10% PEG 8000, 20% ethylene glycol, 20 mM each of 1,6-hexanediol, 1-butanol 1-2-propanediol 2-propanol 1,4-butaediol 1,3-propanediol and 0.1 mM MES/imidazole, pH6.5

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.203	α = 90
b = 106.122	β = 90
c = 112.472	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS3 6M		2018-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	ESRF	ID29

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	1.8	112.47	99.8	0.055	0.06	0.025	0.999	13.9	5.9		91686

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	1.8	1.83	97.8		1.819	1.993	0.805	0.425		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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1EFC	1.8	112.47	87124	4510	99.74	0.199	0.1971	0.21	0.2373	0.2	RANDOM	43.081

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]
0.64			1.03		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.355
r_dihedral_angle_4_deg	19.587
r_dihedral_angle_3_deg	14.342
r_dihedral_angle_1_deg	6.933
r_angle_refined_deg	2.037
r_angle_other_deg	1.059
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.355
r_dihedral_angle_4_deg	19.587
r_dihedral_angle_3_deg	14.342
r_dihedral_angle_1_deg	6.933
r_angle_refined_deg	2.037
r_angle_other_deg	1.059
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5684
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	58

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Auto-Rickshaw	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.