3IEF | pdb_00003ief

Crystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P9P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MPCS	7	293	Initial crystal hit JCSG+ condition G7 15% PEG 3350, 0.1M succinic acid pH 7.0 optimized with microcapillary gradient, MPCS, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.017	α = 90
b = 84.467	β = 90
c = 97.192	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2009-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97946	SSRL	BL7-1

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	2.5	50	99.9	0.116	18.2	8.9		16569

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)
	2.5	2.59	100		0.492	3.8	8.5	1614

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	1p9p	2.5	50	16525	825	99.89	0.196	0.195	0.19	0.225	0.2	RANDOM	30.164

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]
-0.99			-1.98		2.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.112
r_dihedral_angle_4_deg	18.305
r_dihedral_angle_3_deg	15.455
r_dihedral_angle_1_deg	6.039
r_scangle_it	3.296
r_scbond_it	1.999
r_mcangle_it	1.471
r_angle_refined_deg	1.381
r_mcbond_it	0.78
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.112
r_dihedral_angle_4_deg	18.305
r_dihedral_angle_3_deg	15.455
r_dihedral_angle_1_deg	6.039
r_scangle_it	3.296
r_scbond_it	1.999
r_mcangle_it	1.471
r_angle_refined_deg	1.381
r_mcbond_it	0.78
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3287
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms

Software

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

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.