2OD6

Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096682647733) from uncultured marine organism 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, NANODROP	9	277	30.0% PEG-6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.433	α = 90
b = 92.842	β = 90
c = 144.927	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2006-11-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97944, 0.97972	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	29.086	99.8	0.072	0.072	6.1	3.6		42961

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		0.611	0.611	1.2	3.6	3134

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	1.85	29.086	42910	2164	99.68	0.198	0.197	0.231	RANDOM	11.009

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]
4.05			-2.58		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.353
r_dihedral_angle_3_deg	14.267
r_dihedral_angle_4_deg	13.632
r_scangle_it	6.948
r_dihedral_angle_1_deg	6.753
r_scbond_it	5.681
r_mcangle_it	3.122
r_mcbond_it	2.465
r_angle_refined_deg	1.681
r_angle_other_deg	1.061
r_mcbond_other	0.716
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.212
r_nbd_other	0.197
r_nbtor_refined	0.19
r_symmetry_vdw_other	0.184
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.164
r_chiral_restr	0.136
r_nbtor_other	0.093
r_xyhbond_nbd_other	0.031
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3468
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	120

Software

Software
Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling