5HR6

X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia coli

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	PEG 4000, potassium chloride, magnesium chloride, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.664	α = 90
b = 69.821	β = 90.3
c = 149.298	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD		2014-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.85	88.663	99.6	0.132	7.1	6.3		23364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.9	99.6			6.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.88	88.663	39727	1700	98.92	0.18365	0.18175	0.22811	RANDOM	72.823

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]
-1.52		0.56	1.09		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.694
r_dihedral_angle_4_deg	18.056
r_dihedral_angle_3_deg	17.107
r_long_range_B_refined	9.429
r_long_range_B_other	9.428
r_scangle_other	7.171
r_dihedral_angle_1_deg	6.899
r_mcangle_it	5.738
r_mcangle_other	5.737
r_scbond_it	4.978
r_scbond_other	4.977
r_mcbond_it	3.824
r_mcbond_other	3.824
r_angle_refined_deg	1.695
r_angle_other_deg	1.178
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5572
Nucleic Acid Atoms	2845
Solvent Atoms	46
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing