4QPB

Catalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the absence of phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	6 mM pentapeptide GGSGG, 0.1 M Tris (base), Bicine pH 8.5, 0.1 M amino acids (L-Na-glutamate, alanine (racemic), glycine; lysine-HCl (racemic); serine (racemic)), 30% v/v precipitant (ethylene glycol, PEG 8000)., VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.289	α = 90
b = 107.318	β = 97.63
c = 34.307	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	PIXEL	DECTRIS PILATUS 6M		2013-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.78	35	99.1	0.167	7.52	2.74	23389	23389

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.89	98.8		0.586	2.1	2.73	3748

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 4QP5	1.78	33.99	23387	23387	707	99.19	0.21133	0.21025	0.24432	THIN RESOLUTION SHELLS	12.819

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]
-1.36		0.02	1.61		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.937
r_dihedral_angle_4_deg	22.563
r_dihedral_angle_3_deg	13.202
r_dihedral_angle_1_deg	6.904
r_scangle_it	3.932
r_scbond_it	2.679
r_angle_refined_deg	1.754
r_mcangle_it	1.684
r_angle_other_deg	1.388
r_mcbond_it	1.043
r_chiral_restr	0.11
r_bond_refined_d	0.023
r_gen_planes_other	0.013
r_gen_planes_refined	0.01
r_bond_other_d
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2082
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling