2G40

Crystal structure of a duf162 family protein (dr_1909) from deinococcus radiodurans at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	8.3	277	20.0% PEG-3350, 0.2M K3Citrate, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	0.2M MgCl2, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.41	α = 90
b = 53.41	β = 90
c = 118.31	γ = 90

Symmetry
Space Group	P 43 21 2

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 QUANTUM 4		2004-08-26	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315	1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing	2006-01-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3
2	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.918381, 0.979310, 0.978359	SSRL	BL1-5

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	1.7	27.28	98.3	0.067	18.38			19674			25.34

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	1.7	1.76	94.7		0.498	2.8

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	MAD	THROUGHOUT	1.7	27.28	19611	984	99.79	0.18	0.178	0.22	RANDOM	19.501

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]
-0.28			-0.28		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.646
r_dihedral_angle_4_deg	19.185
r_dihedral_angle_3_deg	10.805
r_dihedral_angle_1_deg	6.218
r_scangle_it	5.939
r_scbond_it	4.089
r_mcangle_it	2.317
r_mcbond_it	1.716
r_angle_refined_deg	1.344
r_angle_other_deg	0.78
r_mcbond_other	0.434
r_symmetry_vdw_other	0.246
r_nbd_refined	0.211
r_nbd_other	0.185
r_symmetry_hbond_refined	0.177
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.147
r_nbtor_other	0.081
r_symmetry_vdw_refined	0.079
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1216
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing