4GG9 | pdb_00004gg9

tRNA Guanine Transglycosylase in complex with thiophene-substituted lin-benzohypoxanthine inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P0D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	288	100 MM MES, 1MM DTT, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.33	49.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.167	α = 90
b = 64.983	β = 96.19
c = 70.734	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	CCD	RAYONIX MX-225	Rh-coated silicon with indirect water cooling	2010-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.48	30	98.5	0.043	19.52	2.9	67886	67886			15.74

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.51	94.7		0.269	3.49	2.6	3191

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	AB INITIO PHASING	FREE R	1P0D	1.48	30	64852	61547	3305	94.8	0.1407	0.1407	0.1395	0.15	0.1884	0.16	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
6	2619	3019

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.078
s_zero_chiral_vol	0.056
s_non_zero_chiral_vol	0.053
s_similar_adp_cmpnt	0.047
s_anti_bump_dis_restr	0.028
s_angle_d	0.027
s_from_restr_planes	0.0237
s_bond_d	0.01
s_rigid_bond_adp_cmpnt	0.003
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2671
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.