- PDB-3t69: Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3t69
Title
Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase protein from Sinorhizobium meliloti
Components
Putative 2-dehydro-3-deoxygalactonokinase
Keywords
TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / 2-dehydro-3-deoxygalactonokinase
Function / homology
Function and homology information
2-dehydro-3-deoxygalactonokinase / 2-dehydro-3-deoxygalactonokinase activity / D-galactonate catabolic process / ATP binding Similarity search - Function
Resolution: 2.6→2.69 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5 / % possible all: 100
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Processing
Software
Name
Version
Classification
CBASS
datacollection
SHELXD
phasing
SHARP
phasing
CCP4
modelbuilding
Coot
modelbuilding
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
CCP4
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.55→43.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.082 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27739
1360
5 %
RANDOM
Rwork
0.21741
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-
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obs
0.22032
25837
97.16 %
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all
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26367
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 48.275 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.07 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
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-0.06 Å2
Refinement step
Cycle: LAST / Resolution: 2.55→43.46 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4402
0
25
64
4491
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.021
4502
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.88
1.948
6127
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.946
5
601
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.908
22.444
180
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.178
15
652
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.303
15
40
X-RAY DIFFRACTION
r_chiral_restr
0.13
0.2
707
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
3423
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.911
1.5
2971
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.752
2
4667
X-RAY DIFFRACTION
r_scbond_it
2.784
3
1531
X-RAY DIFFRACTION
r_scangle_it
4.608
4.5
1460
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.545→2.611 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.404
61
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Rwork
0.288
1300
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obs
-
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66.59 %
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