4IFA | pdb_00004ifa

1.5 Angstrom resolution crystal structure of an extracellular protein containing a SCP domain from Bacillus anthracis str. Ames

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	protein at 7.7 mg/mL in 10 mM Tris-HCL pH 8.3 500 mM NaCl, 5 mM BME, crystallization: The Classics II Suite (condition G11: 200 mM Mg Cl2, 100 mM Bis-Tris pH 6.5, 25% (w/v) PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.115	α = 90
b = 86.118	β = 90
c = 89.02	γ = 90

Symmetry
Space Group	P 21 21 21

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 300 mm CCD	Be Lenses	2012-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	30	99.9	0.078	47	7.2	56956	56956	-3		22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		0.53	3.8	7.1	2809

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.5	29.67	54572	54572	2908	99.89	0.15504	0.15353	0.1547	0.18304	0.1832	RANDOM	23.292

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]
1.99			-1.37		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.081
r_dihedral_angle_4_deg	15.302
r_dihedral_angle_3_deg	10.3
r_dihedral_angle_1_deg	4.286
r_scangle_it	3.638
r_scbond_it	2.366
r_angle_refined_deg	1.524
r_mcangle_it	1.5
r_mcbond_it	0.921
r_angle_other_deg	0.912

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.081
r_dihedral_angle_4_deg	15.302
r_dihedral_angle_3_deg	10.3
r_dihedral_angle_1_deg	4.286
r_scangle_it	3.638
r_scbond_it	2.366
r_angle_refined_deg	1.524
r_mcangle_it	1.5
r_mcbond_it	0.921
r_angle_other_deg	0.912
r_mcbond_other	0.307
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2416
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	38

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.