5HR7 | pdb_00005hr7

X-ray crystal structure of C118A RlmN from Escherichia coli with cross-linked in vitro transcribed tRNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RFA	3RFA,2DER
experimental model	PDB	2DER	3RFA,2DER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	298	PEG 4000, sodium chloride, sodium cacodylate trihydrate, spermine

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.717	α = 90
b = 70.383	β = 90.11
c = 151.81	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		2014-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	50	99.9	0.087	0.8	34.9	7.3		75380

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	99.2		0.529	1.8	5.7

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	3RFA,2DER	2.4	50	71560	3788	99.68	0.2174	0.2158	0.22	0.2475	0.25	RANDOM	62.237

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]
0.01		-0.01	0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.606
r_dihedral_angle_3_deg	13.189
r_dihedral_angle_4_deg	12.467
r_dihedral_angle_1_deg	5.919
r_mcangle_it	3.299
r_mcbond_it	1.988
r_mcbond_other	1.988
r_angle_other_deg	1.612
r_angle_refined_deg	1.01
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.606
r_dihedral_angle_3_deg	13.189
r_dihedral_angle_4_deg	12.467
r_dihedral_angle_1_deg	5.919
r_mcangle_it	3.299
r_mcbond_it	1.988
r_mcbond_other	1.988
r_angle_other_deg	1.612
r_angle_refined_deg	1.01
r_chiral_restr	0.075
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5678
Nucleic Acid Atoms	2972
Solvent Atoms	94
Heterogen Atoms	77

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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.