KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, GLU 45 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 45 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, GLU 45 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 45 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLU 45 TO ASN
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 1.99 Å3/Da / Density % sol: 37.67 %
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection
Resolution: 1.55→40 Å / Num. obs: 82974 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shell
Resolution: 1.55→1.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 97
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0007
refinement
MOSFLM
datareduction
SCALA
datascaling
CCP4
phasing
Refinement
Method to determine structure: MIR / Resolution: 1.55→40.16 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.05 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS ADDITIONAL DENSITY IN SOME SUBUNITS FOR A CARBINOLAMINE ATTACHED TO THE ACTIVE SITE LYSINE 133. INCLUSION IN THE MODEL DID NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS ADDITIONAL DENSITY IN SOME SUBUNITS FOR A CARBINOLAMINE ATTACHED TO THE ACTIVE SITE LYSINE 133. INCLUSION IN THE MODEL DID NOT GIVE A SATISFACTORY MAP OR MODEL AFTER REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.217
4409
5 %
RANDOM
Rwork
0.168
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obs
0.17
82974
98 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK