Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
THE COA MIMIC INHIBITOR CAJ IS BOUND AT CYS 43 WITH A COVALENT BOND BETWEE CBU AOF CA6 AND SG OF ...THE COA MIMIC INHIBITOR CAJ IS BOUND AT CYS 43 WITH A COVALENT BOND BETWEE CBU AOF CA6 AND SG OF CYS. THE PRE-REACTION COMPOUND HAD A DOUBLE BOND BETWEEN CBU AND CBV WHICH OPENED UP TO FORM THE COVALENT LINKAGE WITH CYS SIDE CHAIN UPON REACTION.
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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 400, magnesium chloride, HEPES, NADP+, pH 7.2, Vapor Diffusion, Sitting Drop, temperature 293K, EtVC-CoA, VAPOR DIFFUSION, SITTING DROP
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2011
Radiation
Monochromator: Double crystal with K-B biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.39→91.28 Å / Num. obs: 34628 / % possible obs: 98.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Diffraction-ID
% possible all
2.4-2.44
6.4
0.401
1
97
2.44-2.49
6.5
0.381
1
96.4
2.49-2.53
6.7
0.369
1
96.8
2.53-2.59
7
0.348
1
97.2
2.59-2.64
7.2
0.333
1
97
2.64-2.7
7.2
0.478
1
97.5
2.7-2.77
7.4
0.275
1
97
2.77-2.85
7.5
0.238
1
97.8
2.85-2.93
7.5
0.218
1
97.7
2.93-3.02
7.6
0.19
1
97.8
3.02-3.13
7.6
0.168
1
98.5
3.13-3.26
7.6
0.151
1
98.6
3.26-3.41
7.6
0.138
1
98.5
3.41-3.58
7.6
0.154
1
98.8
3.58-3.81
7.3
0.146
1
99
3.81-4.1
7.3
0.123
1
99
4.1-4.52
7.4
0.085
1
99
4.52-5.17
7.4
0.077
1
98.9
5.17-6.51
7.5
0.075
1
99.3
6.51-50
7.2
0.105
1
99.3
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.6.0117
refinement
PHASER
phasing
PHENIX
refinement
PDB_EXTRACT
3.11
dataextraction
HKL-2000
datacollection
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Resolution: 2.39→91.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.867 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21841
1709
5 %
RANDOM
Rwork
0.16432
-
-
-
obs
0.167
32753
96.93 %
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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
Displacement parameters
Biso mean: 33.669 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.01 Å2
0 Å2
-0.19 Å2
2-
-
4.04 Å2
-0 Å2
3-
-
-
-3.13 Å2
Refinement step
Cycle: LAST / Resolution: 2.39→91.28 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6805
0
217
218
7240
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.02
7197
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.816
1.99
9797
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.635
5
870
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.436
24.495
327
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.649
15
1176
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.555
15
39
X-RAY DIFFRACTION
r_chiral_restr
0.111
0.2
1104
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
5403
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.389→2.451 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.246
98
-
Rwork
0.187
2095
-
obs
-
-
86.71 %
+
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