3B40 | pdb_00003b40

Crystal structure of the probable dipeptidase PvdM from Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	100mM Hepes pH 7.0, 3% PEG 3350, 5mM Calcium chloride, 5mM Nickel chloride hexahydrate, 5mM Magnesium chloride hexahydrate, 5mM Cadmium chloride, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.123	α = 90
b = 147.123	β = 90
c = 147.123	γ = 90

Symmetry
Space Group	I 2 3

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	MAR CCD 165 mm		2007-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	24.52	99.9	0.172	0.172	16.4	12.1	35783	35783			19.1

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)
	2	2.11	100		0.359	0.359	6.4	11.6	5166

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	20	35720	35720	1788	99.89	0.194	0.192	0.19	0.233	0.24	RANDOM	20.301

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.536
r_dihedral_angle_4_deg	18.404
r_dihedral_angle_3_deg	14.81
r_dihedral_angle_1_deg	6.071
r_scangle_it	3.506
r_scbond_it	2.237
r_angle_refined_deg	1.439
r_mcangle_it	1.205
r_mcbond_it	0.772
r_metal_ion_refined	0.394
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.152
r_symmetry_hbond_refined	0.108
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3126
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building