3PYL

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529820 % 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 coefficientSolvent content
2.1943.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.115α = 90
b = 78.155β = 90
c = 246.061γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002008-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.247.07900.06718.53.86482232.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2880.80.19152.45748

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.247.0761536325589.480.200580.198250.246RANDOM31.798
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]
0.01-0.640.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.536
r_dihedral_angle_4_deg20.311
r_dihedral_angle_3_deg15.054
r_dihedral_angle_1_deg5.636
r_scangle_it1.896
r_scbond_it1.124
r_angle_refined_deg1.085
r_mcangle_it0.735
r_mcbond_it0.385
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.536
r_dihedral_angle_4_deg20.311
r_dihedral_angle_3_deg15.054
r_dihedral_angle_1_deg5.636
r_scangle_it1.896
r_scbond_it1.124
r_angle_refined_deg1.085
r_mcangle_it0.735
r_mcbond_it0.385
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms10879
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms21

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling