4LXC | pdb_00004lxc

The antimicrobial peptidase lysostaphin from Staphylococcus simulans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R77	pdb entries 1R77, 2B0P
experimental model	PDB	2B0P	pdb entries 1R77, 2B0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M MES and 1.6 M magnesium sulphate, 2 mM tetraglycine phosphinic acid. EDTA and ammonium sulphate as additives improved crystal quality, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
8.29	85.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 282.013	α = 90
b = 282.013	β = 90
c = 282.013	γ = 90

Symmetry
Space Group	P 43 3 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	DECTRIS PILATUS 6M		2013-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

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	3.5	50	100	0.295	0.295	17.34	36.4	48693	48693			36.3

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	3.5	3.59	100		0.908	0.908	5.34	37.9	3539

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 1R77, 2B0P	3.5	47.67	48689	48689	2435	100	0.26873	0.26777	0.25	0.28684	0.26	RANDOM	40.566

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.969
r_dihedral_angle_3_deg	17.977
r_dihedral_angle_4_deg	9.819
r_dihedral_angle_1_deg	6.457
r_angle_other_deg	4.421
r_angle_refined_deg	1.193
r_symmetry_vdw_other	0.252
r_nbd_other	0.231
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.211
r_nbtor_refined	0.195
r_metal_ion_refined	0.182
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.142
r_nbtor_other	0.118
r_chiral_restr	0.066
r_gen_planes_other	0.035
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	7540
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	49

Software

Software
Software Name	Purpose
CBFlib	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling