4NV4 | pdb_00004nv4

1.8 Angstrom Crystal Structure of Signal Peptidase I from Bacillus anthracis.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ME8	PDB ENTRY 4ME8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 7.3 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2	38.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.225	α = 90
b = 80.225	β = 90
c = 174.25	γ = 120

Symmetry
Space Group	P 63 2 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	MARMOSAIC 225 mm CCD	Beryllium lenses	2013-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.8	30	99.8	0.056	0.056	30	7.1	31574	31574		-3	27.2

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	1.8	1.83	100		0.512	0.512	3.9	7.2	1542

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 (All)	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 ENTRY 4ME8	1.8	29.81	29946	29946	1591	99.76	0.17403	0.17403	0.17272	0.18	0.1994	0.21	RANDOM	35.616

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]
0.56	0.28		0.56		-1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.514
r_dihedral_angle_4_deg	12.077
r_dihedral_angle_3_deg	11.49
r_long_range_B_refined	7.609
r_long_range_B_other	7.514
r_scangle_other	4.628
r_dihedral_angle_1_deg	4.454
r_scbond_it	3.007
r_scbond_other	3.001
r_mcangle_other	2.85
r_mcangle_it	2.849
r_mcbond_it	1.88
r_mcbond_other	1.87
r_angle_refined_deg	1.558
r_angle_other_deg	0.736
r_chiral_restr	0.114
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1865
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	61

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling