3BH1

Crystal structure of protein DIP2346 from Corynebacterium diphtheriae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	294	100mM Bis-Tris pH 6.0, 30% PEG 3350, 200mM Ammonium acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.453	α = 90
b = 138.936	β = 116.49
c = 98.266	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MAR CCD 165 mm		2005-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

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	2.51	50	97.6	0.1	0.081	4.4	2.6		78192		-0.5	59.6

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	2.51	2.61	81.1		0.58	1.1	2.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.51	20	75434	1542	98.68	0.21188	0.21068	0.27134	RANDOM	62.536

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]
-0.83		-1.52	-1.37		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.383
r_dihedral_angle_3_deg	19.233
r_dihedral_angle_4_deg	15.37
r_scangle_it	14.903
r_scbond_it	11.831
r_mcangle_it	7.336
r_mcbond_it	5.348
r_dihedral_angle_1_deg	5.289
r_angle_refined_deg	1.146
r_nbtor_refined	0.292
r_symmetry_hbond_refined	0.213
r_xyhbond_nbd_refined	0.138
r_nbd_refined	0.135
r_symmetry_vdw_refined	0.124
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	15076
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	24

Software

Software
Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing