4B5U

Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with pyruvate and succinic semialdehyde


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V5JPDB ENTRY 2V5J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.5 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% GLYCEROL, 2 MM COCL2 PH 5
Crystal Properties
Matthews coefficientSolvent content
4.0269.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.13α = 90
b = 151.13β = 90
c = 151.13γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
11.9141.998.60.0321.121.887289118.75
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)
11.911.9681.70.242.94.9

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 2V5J1.91341.916287275654698.640.13220.13040.153923.9
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.824
f_angle_d1.387
f_chiral_restr0.087
f_bond_d0.014
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3800
Nucleic Acid Atoms
Solvent Atoms808
Heterogen Atoms42

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXphasing