3DCX | pdb_00003dcx

Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.83	277	37.0% 2-methyl-2,4-pentanediol, 0.15M sodium chloride, 0.1M HEPES pH 6.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.07	α = 90
b = 75.32	β = 90
c = 139.4	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)	2008-04-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97925,0.91837,0.97871	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	29.828	97.9	0.056	11.19	4.05		43831		-3	31.07

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	2.07	95.9		0.638	1.5

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	2	29.828	43782	2200	98.93	0.186	0.184	0.19	0.227	0.23	RANDOM	25.932

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]
0.86			-0.94		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.851
r_dihedral_angle_4_deg	15.15
r_dihedral_angle_3_deg	14.384
r_scangle_it	6.697
r_dihedral_angle_1_deg	6.206
r_scbond_it	4.88
r_mcangle_it	2.667
r_mcbond_it	1.993
r_angle_refined_deg	1.413
r_angle_other_deg	0.895
r_mcbond_other	0.722
r_symmetry_vdw_other	0.221
r_symmetry_hbond_refined	0.214
r_symmetry_vdw_refined	0.208
r_nbd_refined	0.198
r_nbd_other	0.194
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.16
r_nbtor_other	0.084
r_chiral_restr	0.079
r_bond_refined_d	0.014
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	4366
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	57

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