3DSB | pdb_00003dsb

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	0.1M Ammonium Sulfate 0.1M Tris-Sodium Citrate, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.488	α = 90
b = 66.765	β = 90
c = 133.884	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	ADSC QUANTUM 315	Mirror	2008-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97932	APS	19-ID

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	1.48	37.1	98.4	0.099	42.4	7.4	62315	62315

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	1.48	1.51	90.7		0.462	4	6	2787

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	1.48	37.1	59077	59077	3156	98.49	0.17017	0.17017	0.16828	0.17	0.20526	0.2	RANDOM	20.509

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]
0.06			-0.1		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.373
r_dihedral_angle_3_deg	13.464
r_dihedral_angle_4_deg	10.696
r_sphericity_free	6.853
r_dihedral_angle_1_deg	6.142
r_sphericity_bonded	5.879
r_scangle_it	4.779
r_scbond_it	3.71
r_mcangle_it	2.443
r_rigid_bond_restr	2.301
r_mcbond_it	1.725
r_angle_refined_deg	1.545
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.252
r_symmetry_hbond_refined	0.241
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.127
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2588
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing