3FS2

Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis at 1.85A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FWSpdb coordinate set 1fws, monomer after sidechain adjustment with chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290JCSG+ SCREEN D3: 100MM NA/K PHOSPHATE PH 6.2, 50% PEG 200, 200MM NACL, PH 5.5, VAPOR DIFFUSION, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1843.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.53α = 90
b = 75.64β = 126
c = 74.65γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDWESTBROOK NOIR2008-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.000ALS4.2.2

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
11.855097.70.07810.223.54591645916-329.4
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)
1.851.987.10.4812.62.63021

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTpdb coordinate set 1fws, monomer after sidechain adjustment with chainsaw1.8519.174591445914236698.30.1790.1790.1760.222RANDOM20.39
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]
-0.180.180.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.924
r_dihedral_angle_4_deg18.241
r_dihedral_angle_3_deg13.109
r_dihedral_angle_1_deg5.994
r_scangle_it4.376
r_scbond_it2.682
r_mcangle_it1.773
r_angle_refined_deg1.591
r_mcbond_it1.007
r_angle_other_deg0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.924
r_dihedral_angle_4_deg18.241
r_dihedral_angle_3_deg13.109
r_dihedral_angle_1_deg5.994
r_scangle_it4.376
r_scbond_it2.682
r_mcangle_it1.773
r_angle_refined_deg1.591
r_mcbond_it1.007
r_angle_other_deg0.993
r_mcbond_other0.275
r_chiral_restr0.097
r_bond_refined_d0.017
r_gen_planes_refined0.007
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 Atoms3778
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms40

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling