2I8C

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.802	α = 90
b = 66.972	β = 96.05
c = 78.992	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 210	mirror	2001-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-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	2.46	79	99	0.07	0.07	23.9	3.7	25017	23741			40

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	2.5	2.59	99.2		0.621	0.621	2	3.7	1329

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2I87	2.46	47.51	25017	23741	1254	97.18	0.21283	0.20988	0.26926	RANDOM	45.406

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]
2.43		-1.44			-2.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.023
r_dihedral_angle_4_deg	21.081
r_dihedral_angle_3_deg	19.356
r_dihedral_angle_1_deg	7.761
r_scangle_it	3
r_scbond_it	2.019
r_angle_refined_deg	1.776
r_mcangle_it	1.262
r_mcbond_it	1.049
r_angle_other_deg	0.981
r_symmetry_vdw_other	0.255
r_nbd_refined	0.232
r_nbd_other	0.206
r_nbtor_refined	0.193
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.189
r_mcbond_other	0.156
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.095
r_nbtor_other	0.095
r_xyhbond_nbd_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5496
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement