Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
MALONATE ION (MLI): USED AS A CRYSTALLIZATION REAGENT LIGAND V1N IS A SUBSTRATE MIMETIC INHIBITOR
Sequence details
LAST 11 RESIDUES ARE PART OF A HIS-TAG ADDED TO THE PROTEIN
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
Density Matthews: 2.7 Å3/Da / Density % sol: 53.5 % Description: STRUCTURE WAS SOLVED INITIALLY WTH A SINGLE PT DERIVATIVE AND LATER REFINED TO HIGHER RESOLUTION, 2.40 A, USING A SECOND NATIVE DATA SET.
Crystal grow
Temperature: 293 K / pH: 7 Details: THE PROTEIN WAS CONCENTRATED TO 6 MG/ML IN THE PRESENCE OF 10 MM INHIBITOR AND CRYSTALLIZED AT 20 DEGREES CELSIUS IN 0.7 TO 1.0 M SODIUM MALONATE.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9537 Å / Relative weight: 1
Reflection
Resolution: 2.37→338.07 Å / Num. obs: 59192 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.4
Reflection shell
Resolution: 2.37→2.5 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.7 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
XDS
datareduction
SCALA
datascaling
Auto-Rickshaw
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.794 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE NOT MODELLED UNLESS THERE WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE NOT MODELLED UNLESS THERE WAS SUFFICIENT DENSITY FOR AT LEAST THE BACKBONE
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26387
2919
5.1 %
RANDOM
Rwork
0.22445
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obs
0.22646
54126
99.99 %
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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: MASK