9LRI | pdb_00009lri

Crystal Structure of Thermus thermophilus KhpB/EloR complexed with RNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M HEPES (pH 7.5), 0.2M ammonium sulfate, 25% (w/v) polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.261	α = 97.34
b = 46.058	β = 92.53
c = 56.885	γ = 112.693

Symmetry
Space Group	P 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	CCD	RAYONIX MX225HE		2017-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	2.65	36.99	97.7	0.09	0.103	0.031	0.999	30.1	8.3		10994			62.02

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	2.65	2.75	97.3		0.2	0.231	0.088	0.902		7.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.65	32.382	9273	492	97.724	0.207	0.2036	0.207	0.2653	0.265	38.027

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]
-0.036	0.016	0.088	0.055	0.088	-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.129
r_dihedral_angle_6_deg	15.63
r_lrange_it	8.763
r_lrange_other	8.763
r_scangle_it	6.311
r_scangle_other	6.309
r_dihedral_angle_1_deg	5.686
r_dihedral_angle_2_deg	5.308
r_mcangle_it	5.061
r_mcangle_other	5.06
r_scbond_it	4.169
r_scbond_other	4.167
r_mcbond_it	3.291
r_mcbond_other	3.289
r_angle_refined_deg	1.172
r_angle_other_deg	0.384
r_symmetry_xyhbond_nbd_refined	0.268
r_symmetry_nbd_refined	0.264
r_nbd_refined	0.228
r_nbd_other	0.2
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.169
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.054
r_dihedral_angle_other_2_deg	0.028
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2301
Nucleic Acid Atoms	140
Solvent Atoms	5
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing