4KYX | pdb_00004kyx

Crystal structure of ADP-ribose pyrophosphatase MutT from Rickettsia felis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	JCSG screen, condition H10: 25% PEG 3350, 200mM ammonium acetate, 100mM BisTris pH 5.5; RifeA.17522.a.B1.PW36475 at 28.18 mg/ml, tray 241401h10; crystal incubated in 375mM NaI / 7.5% EG, and 750mM NaI / 15% EG; this crystal was used for phasing, VAPOR DIFFUSION, SITTING DROP, temperature 290K
2	VAPOR DIFFUSION, SITTING DROP	7.5	290	JCSG screen, condition A5: 20% PEG 3350, 200mM magnesium formate; RifeA.17522.a.B1.PW36475 at 28.18 mg/ml, tray 241401a5; cryo: 10/20% EG; this crystal was used for refinement, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.7
2	38.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.98	α = 90
b = 63.78	β = 90
c = 71.72	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	RIGAKU SATURN 944+		2013-04-09	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 210r		2013-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95370	Australian Synchrotron	MX1

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	1.8	50	98.4	0.041	30.74	7	26627	26202		-3	26.836

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	1.8	1.85	96		0.261	6.97

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	46.5	26627	24862	1291	98.42	0.2149	0.2128	0.2556	0.2501	RANDOM	25.2832

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]
0.57			0.37		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_4_deg	14.677
r_dihedral_angle_3_deg	12.348
r_dihedral_angle_1_deg	6.526
r_mcangle_it	1.761
r_angle_refined_deg	1.612
r_mcbond_it	1.008
r_mcbond_other	1.001
r_angle_other_deg	0.824
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2180
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction