3EEU

Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	4	298	PEG 4000, Na acetate, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.212	α = 90
b = 70.212	β = 90
c = 99.915	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	RIGAKU RAXIS4		2006-05-26	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	50	99.9	0.039	43.438	5.4		19802

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	2.07	100		0.775		5.2	1934

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	30.4	19758	999	99.92	0.218	0.216	0.256	RANDOM	45.414

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]
-0.4	-0.2		-0.4		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.965
r_dihedral_angle_3_deg	16.128
r_dihedral_angle_4_deg	14.236
r_dihedral_angle_1_deg	6.009
r_scangle_it	2.407
r_scbond_it	1.654
r_angle_refined_deg	1.361
r_mcangle_it	0.966
r_mcbond_it	0.621
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.257
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.162
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.097
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_metal_ion_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2127
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	11

Software

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