3PYL

Crystal structure of aspartate beta-semialdehide dehydrogenase from Streptococcus pneumoniae with D-2,3-diaminopropionate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	20 % PEG 3350, 0.1 M MES, 0.1 M ammonium acetate, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.115	α = 90
b = 78.155	β = 90
c = 246.061	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	RAYONIX MX-300		2008-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	47.07	90	0.067	18.5	3.8		64822			32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	80.8		0.191	5	2.4	5748

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	FOURIER SYNTHESIS	THROUGHOUT	2.2	47.07	61536	3255	89.48	0.20058	0.19825	0.246	RANDOM	31.798

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]
0.01			-0.64		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.536
r_dihedral_angle_4_deg	20.311
r_dihedral_angle_3_deg	15.054
r_dihedral_angle_1_deg	5.636
r_scangle_it	1.896
r_scbond_it	1.124
r_angle_refined_deg	1.085
r_mcangle_it	0.735
r_mcbond_it	0.385
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	10879
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	21

Software

Software
Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling