3BDV

Crystal structure of a putative yden-like hydrolase (eca3091) from pectobacterium atrosepticum scri1043 at 1.66 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	NANODROP, 0.2M Ca(OAc)2, 10.0% PEG 8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.655	α = 90
b = 93.302	β = 90
c = 104.095	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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.91840, 0.97953, 0.97939	APS	23-ID-D

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	1.66	42.563	99.7	0.069	10.16			41954		-3	19.61

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	1.66	1.72	99.7		0.539	2.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.66	42.563	41889	2112	99.75	0.173	0.17	0.213	RANDOM	19.964

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]
0.67			-1.48		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.857
r_dihedral_angle_3_deg	13.691
r_dihedral_angle_4_deg	13.559
r_scangle_it	5.683
r_dihedral_angle_1_deg	5.114
r_scbond_it	4.183
r_mcangle_it	2.698
r_mcbond_it	1.962
r_angle_refined_deg	1.485
r_angle_other_deg	0.991
r_mcbond_other	0.657
r_symmetry_vdw_other	0.296
r_nbd_refined	0.221
r_nbd_other	0.214
r_symmetry_vdw_refined	0.213
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.096
r_metal_ion_refined	0.092
r_symmetry_metal_ion_refined	0.089
r_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2997
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing