3EF5

Structure of the RNA pyrophosphohydrolase BdRppH in complex with dGTP

X-RAY DIFFRACTION

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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
3.08	60.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.446	α = 90
b = 68.448	β = 90
c = 92.74	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	CCD	adsc Q210		2008-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0	NSLS	X6A

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	2.4	46.37	89.2	0.049	32.267	6.6		15730

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	2.49	40.7		0.691		4.4	695

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	2.6	46.37	13703	686	98.32	0.243	0.24	0.297	RANDOM	58.584

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]
2.15			2.57		-4.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.206
r_dihedral_angle_4_deg	18.665
r_dihedral_angle_3_deg	18.398
r_dihedral_angle_1_deg	6.326
r_scangle_it	1.796
r_angle_refined_deg	1.246
r_scbond_it	1.092
r_mcangle_it	0.747
r_mcbond_it	0.439
r_nbtor_refined	0.309
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.133
r_symmetry_hbond_refined	0.122
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2131
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
AMoRE	phasing