3B2Y | pdb_00003b2y

CRYSTAL STRUCTURE OF a putative metallopeptidase (SDEN_2526) FROM SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.07	277	NANODROP, 20.4% PEG 6000, 0.1M MES pH 6.07, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.715	α = 90
b = 127.577	β = 116.28
c = 49.303	γ = 90

Symmetry
Space Group	P 1 21 1

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	KOHZU, Double crystal Si(111)	2007-09-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794, 1.0000, 0.9797	ALS	8.2.1

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	1.74	28.82	94.7	0.047	0.047	7.6	1.9		46761			28.085

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	1.74	1.79	95.4		0.38	0.38	2	1.7	3475

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	1.74	28.82	46725	2353	94.32	0.176	0.175	0.18	0.215	0.22	RANDOM	28.462

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]
0.82		1.49	-1.84		2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.16
r_dihedral_angle_4_deg	15.357
r_dihedral_angle_3_deg	13.771
r_scangle_it	8.064
r_dihedral_angle_1_deg	6.263
r_scbond_it	6.017
r_mcangle_it	3.614
r_mcbond_it	2.651
r_angle_refined_deg	1.669
r_angle_other_deg	1.143
r_mcbond_other	0.764
r_symmetry_vdw_other	0.232
r_nbd_refined	0.208
r_nbd_other	0.199
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_refined	0.174
r_symmetry_hbond_refined	0.162
r_chiral_restr	0.128
r_metal_ion_refined	0.096
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4016
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	2

Software

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