3GA9 | pdb_00003ga9

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD, crystal form II

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	12.5% PEGS 3350, 0.1M LiSO4, 0.1M Na Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.704	α = 90
b = 72	β = 90
c = 128.853	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	2006-12-19	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	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	2.28	50	98	0.121	20.4	8.7	23226	22962

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	2.28	2.37	98.6		0.753	1.92	7.2

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	2.3	44.74	19203	19203	1022	99.08	0.20002	0.19717	0.2134	0.25227	0.277	RANDOM	57.379

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]
-0.43			0.72		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.349
r_dihedral_angle_3_deg	16.576
r_dihedral_angle_4_deg	12.693
r_dihedral_angle_1_deg	8.354
r_scangle_it	2.354
r_scbond_it	1.583
r_angle_refined_deg	1.503
r_angle_other_deg	1.061
r_mcangle_it	1.016
r_mcbond_it	0.83
r_chiral_restr	0.218
r_symmetry_vdw_other	0.214
r_nbd_refined	0.21
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.17
r_symmetry_vdw_refined	0.128
r_mcbond_other	0.113
r_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3507
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	19

Software

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