2OTM

Crystal structure of a putative endoribonuclease (so_1960) from shewanella oneidensis mr-1 at 1.85 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 0.16M Ca(OAc)2, 20.0% Glycerol, 14.4% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.083	α = 90
b = 62.908	β = 93.24
c = 78.689	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-01-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97931, 0.97885	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.85	29.21	100	0.105	0.105	5.9	3.8		46806			19.11

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	100		0.667	0.667	1.1	3.8	3463

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.85	29.21	46806	2366	99.95	0.152	0.152	0.151	0.177	RANDOM	19.687

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]
0.21		-0.17	1.02		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.977
r_dihedral_angle_4_deg	15.382
r_dihedral_angle_3_deg	12.795
r_scangle_it	6.541
r_dihedral_angle_1_deg	6.259
r_scbond_it	4.462
r_mcangle_it	2.49
r_angle_refined_deg	1.484
r_mcbond_it	1.394
r_angle_other_deg	0.96
r_symmetry_vdw_refined	0.737
r_mcbond_other	0.358
r_symmetry_vdw_other	0.343
r_symmetry_metal_ion_refined	0.251
r_nbd_refined	0.204
r_nbd_other	0.2
r_nbtor_refined	0.177
r_metal_ion_refined	0.17
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.091
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3448
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	34

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing