3LAT

Crystal structure of Staphylococcus peptidoglycan hydrolase AmiE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	22% butanediol, 0.1M imidazole, 0.15M zinc acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.453	α = 90
b = 99.453	β = 90
c = 148.783	γ = 90

Symmetry
Space Group	P 43 21 2

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 225 mm CCD		2007-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99990	SLS	X06SA

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	1.7	40	99.4	0.09	19.6	10		82089			24.4

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)
	1.7	1.76			0.33	0.33	2.4	6.2	8081

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	SIR	THROUGHOUT	1.7	30.77	77827	4164	99.42	0.14416	0.143	0.16518	RANDOM	28.645

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.377
r_dihedral_angle_3_deg	11.686
r_dihedral_angle_4_deg	9.365
r_dihedral_angle_1_deg	5.736
r_scangle_it	3.481
r_scbond_it	2.507
r_mcangle_it	1.437
r_angle_refined_deg	1.071
r_mcbond_it	0.881
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.21
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.125
r_symmetry_hbond_refined	0.115
r_symmetry_metal_ion_refined	0.081
r_chiral_restr	0.077
r_metal_ion_refined	0.06
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3409
Nucleic Acid Atoms
Solvent Atoms	526
Heterogen Atoms	43

Software

Software
Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling