Journal: J.Mol.Biol. / Year: 2006 Title: Direct Evidence for a Glutamate Switch Necessary for Substrate Recognition: Crystal Structures of Lysine Epsilon-Aminotransferase (Rv3290C) from Mycobacterium Tuberculosis H37Rv. Authors: Tripathi, S.M. / Ramachandran, R.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2→20.53 Å / Num. obs: 38141 / % possible obs: 93 % / Observed criterion σ(I): 20 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shell
Resolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.9 / % possible all: 96.5
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
MOSFLM
datareduction
SCALA
datascaling
AMoRE
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→89.44 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.965 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1-14 ARE DISORDERED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.191
1938
5.1 %
RANDOM
Rwork
0.156
-
-
-
obs
0.158
36201
92.1 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 20.84 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.38 Å2
-0.19 Å2
0 Å2
2-
-
-0.38 Å2
0 Å2
3-
-
-
0.57 Å2
Refinement step
Cycle: LAST / Resolution: 2→89.44 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3350
0
25
230
3605
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
3449
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.593
1.965
4692
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.818
5
434
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.952
22.579
159
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.942
15
532
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.511
15
36
X-RAY DIFFRACTION
r_chiral_restr
0.134
0.2
524
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2677
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.22
0.2
1436
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.306
0.2
2368
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.142
0.2
193
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
0.205
0.2
80
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.097
0.2
24
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
0.929
1.5
2228
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.511
2
3475
X-RAY DIFFRACTION
r_mcangle_other
X-RAY DIFFRACTION
r_scbond_it
2.629
3
1367
X-RAY DIFFRACTION
r_scbond_other
X-RAY DIFFRACTION
r_scangle_it
4.258
4.5
1217
X-RAY DIFFRACTION
r_scangle_other
X-RAY DIFFRACTION
r_long_range_B_refined
X-RAY DIFFRACTION
r_long_range_B_other
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2→2.05 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.272
149
Rwork
0.225
2746
+
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