3IIQ

Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T7D	PDB ENTRY 1T7D CHAIN A WITH LIGANDS REMOVED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.007	α = 90
b = 70.007	β = 90
c = 259.894	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	ADSC QUANTUM 315	MIRRORS	2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	2	67.4	95.2	0.068	0.069	10.4	7.1		40272		2	14

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	2	2.14	95.1		0.43	0.052	5.1	4.3

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	PDB ENTRY 1T7D CHAIN A WITH LIGANDS REMOVED	2	67.4	38237	2035	95.1	0.21	0.207	0.25	RANDOM	40.59

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]
1.17			1.17		-2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_3_deg	15.882
r_dihedral_angle_4_deg	14.229
r_dihedral_angle_1_deg	9.383
r_scangle_it	4.368
r_scbond_it	3.301
r_angle_refined_deg	2.348
r_mcangle_it	2.334
r_mcbond_it	1.824
r_nbtor_refined	0.325
r_chiral_restr	0.321
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.247
r_symmetry_hbond_refined	0.198
r_xyhbond_nbd_refined	0.194
r_bond_refined_d	0.03
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3573
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	114

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling