3FFU

Structure of the RNA pyrophosphohydrolase BdRppH in complex with GTP and magnesium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	7	298	PEG 4000, Na acetate, pH 7, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.732	α = 90
b = 68.749	β = 90
c = 93.069	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	IMAGE PLATE	RIGAKU RAXIS4		2008-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.54

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	2.8	50	98.5	0.054	31.443	3.8		11207

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)
	2.8	2.9	99.8		0.714		3.8	1119

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	2.8	33.61	11171	547	98.61	0.229	0.226	0.301	RANDOM	68.428

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]
1.87			2.28		-4.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.091
r_dihedral_angle_4_deg	23.907
r_dihedral_angle_3_deg	19.483
r_dihedral_angle_1_deg	7.828
r_scangle_it	2.063
r_angle_refined_deg	1.393
r_scbond_it	1.259
r_mcangle_it	0.711
r_mcbond_it	0.369
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.091
r_dihedral_angle_4_deg	23.907
r_dihedral_angle_3_deg	19.483
r_dihedral_angle_1_deg	7.828
r_scangle_it	2.063
r_angle_refined_deg	1.393
r_scbond_it	1.259
r_mcangle_it	0.711
r_mcbond_it	0.369
r_nbtor_refined	0.308
r_nbd_refined	0.212
r_metal_ion_refined	0.194
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.095
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2165
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	70

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.