4OX5

Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.1 M mixture of amino acids (glycine, L-glutamate, and racemates of alanine, serine and lysine), 0.1 M buffer system 2, pH 7.5 and 37.5 % MPD/PEG1000/PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.855	α = 90
b = 60.414	β = 90
c = 138.269	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	PSI PILATUS 6M		2012-09-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

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	1.8	19.95	98.6	34.4	24.3		25656

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	86.9		2.4	14.2

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	SAD	THROUGHOUT	1.8	19.949	18174	955	98.45	0.1933	0.19058	0.25147	RANDOM	42.116

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]
2.75			-0.02		-2.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.336
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_4_deg	13.804
r_long_range_B_refined	12.198
r_long_range_B_other	12.196
r_dihedral_angle_1_deg	6.46
r_scangle_other	6.053
r_mcangle_it	4.764
r_mcangle_other	4.762
r_scbond_it	4.626
r_scbond_other	4.623
r_mcbond_it	3.731
r_mcbond_other	3.712
r_angle_refined_deg	2.003
r_angle_other_deg	0.839
r_chiral_restr	0.249
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1468
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement