2OOK | pdb_00002ook

Crystal structure of a protein with unknown function (YP_749275.1) from Shewanella Frigidimarina NCIMB 400 at 1.80 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	NANODROP, 0.2M Calcium acetate, 20.0% PEG-3350, No Buffer, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.579	α = 90
b = 40.412	β = 92.23
c = 78.05	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)	2007-01-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97910, 0.97879	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	1.8	28.571	96.5	0.056	0.056	13.6	3.8		22625			24.85

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	1.8	1.85	95.3		0.653	0.653	2.1	3.8	1640

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	28.571	22625	1162	96.02	0.186	0.186	0.183	0.19	0.233	0.24	RANDOM	29.171

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]
-2.16		-1.2	2.58		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.917
r_dihedral_angle_4_deg	13.645
r_dihedral_angle_3_deg	11.623
r_scangle_it	5.68
r_dihedral_angle_1_deg	4.704
r_scbond_it	4.445
r_mcangle_it	2.832
r_mcbond_it	2.073
r_angle_refined_deg	1.526
r_angle_other_deg	0.899
r_mcbond_other	0.524
r_symmetry_vdw_other	0.314
r_symmetry_vdw_refined	0.249
r_nbd_refined	0.209
r_nbd_other	0.199
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.176
r_chiral_restr	0.086
r_nbtor_other	0.086
r_bond_refined_d	0.012
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	1963
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	24

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