4OXD

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, SITTING DROP	8	295	0.2 M Ammonium chloride, 0.1 M Hepes pH 8, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 345.954	α = 90
b = 42.549	β = 93.07
c = 79.318	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 2M		2013-03-11		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.916	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	2.8	47.8	98.3	7.8	3.4		47327

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	2.8	2.95	98.3		1.9	3.4

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		THROUGHOUT	2.8	47.8	27113	1457	97.9	0.276	0.273	0.334	RANDOM	43.86

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]
-0.1		1.22			-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.416
r_dihedral_angle_3_deg	13.447
r_dihedral_angle_4_deg	8.276
r_dihedral_angle_1_deg	4.794
r_long_range_B_refined	3.649
r_long_range_B_other	3.649
r_mcangle_it	1.702
r_mcangle_other	1.702
r_scangle_other	1.312
r_mcbond_it	0.952
r_mcbond_other	0.952
r_angle_refined_deg	0.842
r_scbond_it	0.798
r_scbond_other	0.798
r_angle_other_deg	0.677
r_chiral_restr	0.048
r_bond_other_d	0.008
r_bond_refined_d	0.005
r_gen_planes_other	0.004
r_gen_planes_refined	0.003
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	7065
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement