3D82

Crystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella frigidimarina ncimb 400 at 2.05 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	293	0.2000M K2NO3, 20.0000% PEG-3350, No Buffer pH 6., NANODROP, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.92	α = 90
b = 95.14	β = 90
c = 237.37	γ = 90

Symmetry
Space Group	C 2 2 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 collimating mirror, toroid focusing mirror	2008-03-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929,0.97918	SSRL	BL9-2

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	2.05	27.853	97	0.04	11.7			40296		-3	36.405

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	2.05	2.12	83.7		0.35	1.9

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	2.05	27.853	40280	2018	98.65	0.187	0.186	0.212	RANDOM	44.746

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]
0.22			-1.93		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.085
r_dihedral_angle_3_deg	11.805
r_dihedral_angle_4_deg	9.108
r_scangle_it	4.77
r_dihedral_angle_1_deg	4.104
r_scbond_it	3.506
r_mcangle_it	1.833
r_angle_refined_deg	1.632
r_angle_other_deg	1.23
r_mcbond_it	1.132
r_mcbond_other	0.232
r_symmetry_vdw_other	0.175
r_nbd_refined	0.168
r_nbtor_refined	0.162
r_nbd_other	0.142
r_symmetry_vdw_refined	0.123
r_chiral_restr	0.102
r_symmetry_hbond_refined	0.091
r_xyhbond_nbd_refined	0.09
r_nbtor_other	0.072
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4170
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing