5NRH

Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		See publication

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	0.05 to 0.3 M Li2SO4, 0.1 M Bis-Tris pH 5.5 and 15-30% (w/v) PEG 3350, ratio protein:reservoir 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.648	α = 90
b = 61.15	β = 90.17
c = 70.079	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	80	PIXEL	DECTRIS PILATUS3 S 6M		2015-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.917410	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	70.08	97.6	15	4.8		141049

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	See publication	1.3	70.08	133936	7097	97.58	0.14825	0.14591	0.19007	RANDOM	24.763

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]
-0.98		1.52	0.64		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.426
r_dihedral_angle_2_deg	30.341
r_dihedral_angle_4_deg	20.523
r_sphericity_bonded	19.534
r_dihedral_angle_3_deg	13.802
r_dihedral_angle_1_deg	7.711
r_long_range_B_refined	7.277
r_long_range_B_other	7.276
r_scangle_other	6.253
r_scbond_other	5.386
r_scbond_it	5.385
r_rigid_bond_restr	4.711
r_mcangle_other	4.583
r_mcangle_it	4.581
r_mcbond_it	3.726
r_mcbond_other	3.716
r_angle_refined_deg	2.247
r_angle_other_deg	1.444
r_chiral_restr	0.184
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4672
Nucleic Acid Atoms
Solvent Atoms	785
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing