3IMI | pdb_00003imi

2.01 Angstrom resolution crystal structure of a HIT family protein from Bacillus anthracis str. 'Ames Ancestor'

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	30% PEG 8000, 0.2M NH4 Sulfate, 0.1M Na Cacodylate pH 6.5. Paratone-N was used for cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.276	α = 90
b = 46.434	β = 100.61
c = 84.291	γ = 90

Symmetry
Space Group	C 1 2 1

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/Diamond Laue Mono	2009-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97857	APS	21-ID-F

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	2	30	99.9	0.068	14.92	3.8	77248	77248		-3	33.6

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	2	2.03	100		0.507	2.67	3.7	3868

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 (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	SAD	THROUGHOUT	2.01	30	37836	37836	1998	99.28	0.16279	0.16279	0.16091	0.1823	0.19754	0.217	RANDOM	20.402

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]
1.45		-0.17	-0.39		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.28
r_dihedral_angle_3_deg	10.323
r_dihedral_angle_4_deg	10.177
r_scangle_it	4.014
r_dihedral_angle_1_deg	3.877
r_scbond_it	2.616
r_mcangle_it	1.563
r_angle_refined_deg	1.472
r_mcbond_it	0.868
r_angle_other_deg	0.845

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.28
r_dihedral_angle_3_deg	10.323
r_dihedral_angle_4_deg	10.177
r_scangle_it	4.014
r_dihedral_angle_1_deg	3.877
r_scbond_it	2.616
r_mcangle_it	1.563
r_angle_refined_deg	1.472
r_mcbond_it	0.868
r_angle_other_deg	0.845
r_mcbond_other	0.277
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4482
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	29

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CRANK	phasing
SHELXCD	phasing
SHELXE	model building
bp3	model building
SOLOMON	phasing
ARP/wARP	model building
BUCCANEER	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
bp3	phasing
BUCCANEER	phasing

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.