3IEH | pdb_00003ieh

Crystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	10.0000% Glycerol, 5.0000% PEG-1000, 30.0000% PEG-600, 0.1M MES pH 6.0, Additive: 0.006 M Zinc Chloride, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.958	α = 90
b = 80.958	β = 90
c = 87.94	γ = 120

Symmetry
Space Group	P 65

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)	2009-04-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97845,0.97752,0.91837	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	2.45	29.775	99.8	0.166	0.166	11.4	7.6		12080			34.498

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	2.45	2.51	99.8		0.757	0.757	2.7	7.6	885

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	2.45	29.775	12072	578	99.9	0.167	0.164	0.17	0.222	0.22	RANDOM	23.22

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]
-0.72	-0.36		-0.72		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.073
r_dihedral_angle_4_deg	14.713
r_dihedral_angle_3_deg	13.682
r_scangle_it	7.179
r_scbond_it	5.191
r_dihedral_angle_1_deg	4.902
r_mcangle_it	3.001
r_mcbond_it	1.648
r_angle_refined_deg	1.494
r_angle_other_deg	0.894

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.073
r_dihedral_angle_4_deg	14.713
r_dihedral_angle_3_deg	13.682
r_scangle_it	7.179
r_scbond_it	5.191
r_dihedral_angle_1_deg	4.902
r_mcangle_it	3.001
r_mcbond_it	1.648
r_angle_refined_deg	1.494
r_angle_other_deg	0.894
r_mcbond_other	0.372
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2053
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.