3IC1

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VGY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52910.2 M NaCl, 0.1 M NaAcetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.448.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.697α = 90
b = 95.751β = 90
c = 185.426γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315double crystal2009-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.34095.90.08617.84.8361633477322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3499.70.573.14.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VGY2.34023462133237138495.70.1950.1940.25RANDOM32.94
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]
0.351.22-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.083
r_dihedral_angle_4_deg19.568
r_dihedral_angle_3_deg15.229
r_dihedral_angle_1_deg6.409
r_scangle_it3.384
r_scbond_it2.078
r_angle_refined_deg1.429
r_mcangle_it1.34
r_angle_other_deg0.907
r_mcbond_it0.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.083
r_dihedral_angle_4_deg19.568
r_dihedral_angle_3_deg15.229
r_dihedral_angle_1_deg6.409
r_scangle_it3.384
r_scbond_it2.078
r_angle_refined_deg1.429
r_mcangle_it1.34
r_angle_other_deg0.907
r_mcbond_it0.704
r_mcbond_other0.137
r_chiral_restr0.08
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5695
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms41

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling