2GPI | pdb_00002gpi

Crystal structure of a protein of unknown function from duf1488 family (shew_3726) from shewanella loihica pv-4 at 1.60 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	2.0M (NH4)2SO4, 0.1M Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.03	α = 90
b = 83.25	β = 90
c = 58.28	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	2006-03-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97925, 0.97858	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	1.6	29.14	93	0.056	11.37			15507			22.412

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	1.6	1.66	87.7		0.339	2.8

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	MAD	THROUGHOUT	1.6	29.14	15490	778	98.14	0.152	0.151	0.16	0.172	0.19	RANDOM	13.613

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]
-0.53			0.43		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.422
r_dihedral_angle_3_deg	12.112
r_dihedral_angle_4_deg	8.238
r_scangle_it	8.154
r_dihedral_angle_1_deg	6.249
r_scbond_it	5.327
r_mcangle_it	3.213
r_mcbond_it	2.499
r_angle_refined_deg	1.538
r_angle_other_deg	0.955
r_mcbond_other	0.523
r_symmetry_vdw_refined	0.287
r_symmetry_vdw_other	0.226
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.205
r_xyhbond_nbd_refined	0.192
r_nbd_other	0.184
r_nbtor_refined	0.175
r_chiral_restr	0.092
r_nbtor_other	0.084
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	733
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	4

Software

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