2GPJ | pdb_00002gpj

CRYSTAL STRUCTURE OF A SIDEROPHORE-INTERACTING PROTEIN (SPUTCN32_0076) FROM SHEWANELLA PUTREFACIENS CN-32 AT 2.20 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	4.6	277	0.02M CaCl2, 30.0% MPD, 0.1M Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.54	α = 90
b = 100.54	β = 90
c = 67.51	γ = 90

Symmetry
Space Group	P 41 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 315	Flat mirror (vertical focusing)	2006-03-03	M	SINGLE WAVELENGTH

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

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	2.2	28.76	96.8	0.121	8.13			18135			43.254

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	2.2	2.28	89.3		0.763	2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.2	28.76	18093	923	99.93	0.179	0.176	0.18	0.232	0.23	RANDOM	42.581

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]
-0.18			-0.18		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.657
r_dihedral_angle_4_deg	16.343
r_dihedral_angle_3_deg	14.204
r_scangle_it	8.873
r_scbond_it	7.289
r_dihedral_angle_1_deg	5.84
r_mcangle_it	4.163
r_mcbond_it	3.04
r_angle_refined_deg	1.233
r_mcbond_other	0.813
r_angle_other_deg	0.624
r_symmetry_vdw_other	0.282
r_nbd_refined	0.221
r_nbd_other	0.217
r_nbtor_refined	0.191
r_symmetry_hbond_refined	0.181
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.148
r_metal_ion_refined	0.127
r_nbtor_other	0.092
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1910
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	112

Software

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