2I8C | pdb_00002i8c

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I87	PDB ENTRY 2I87

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.22	0.26926	0.2	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