9NLO | pdb_00009nlo

Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S04	PDN ENTRY 3S04

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294.15	25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.8	α = 90
b = 71.8	β = 90
c = 263.31	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	RAYONIX MX-300		2012-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.1047	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.32	52.63	99.7	0.097	0.105	0.039	13	7.2		30863

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.32	2.45	99.8		0.392	0.422	0.154	5.8	7.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.32	35.596	30716	1119	99.266	0.21	0.2086	0.2135	0.2338	0.2343	42.583

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]
0.545			0.545		-1.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.446
r_dihedral_angle_3_deg	12.49
r_dihedral_angle_2_deg	10.448
r_lrange_other	7.911
r_lrange_it	7.908
r_dihedral_angle_1_deg	7.245
r_scangle_it	5.939
r_scangle_other	5.938
r_mcangle_it	5.511
r_mcangle_other	5.509
r_scbond_it	3.786
r_scbond_other	3.785
r_mcbond_it	3.606
r_mcbond_other	3.603
r_angle_refined_deg	1.4
r_angle_other_deg	0.475
r_symmetry_nbd_other	0.197
r_nbd_refined	0.185
r_nbtor_refined	0.179
r_nbd_other	0.139
r_symmetry_nbd_refined	0.133
r_xyhbond_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3478
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing