Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.85 Å3/Da / Density % sol: 33.59 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: LIGAND-FREE PROTEIN CRYSTAL GROWN IN SOLUTION CONTAINING 30% PEG 400, 0.1 M HEPES pH7.5, 0.2 M CaCl2, THEN SOAKED IN MOTHER LIQUOR CONTAINING 0.2M MNCL2 AND 50 mM OXALOACETATE (the substrate) ...Details: LIGAND-FREE PROTEIN CRYSTAL GROWN IN SOLUTION CONTAINING 30% PEG 400, 0.1 M HEPES pH7.5, 0.2 M CaCl2, THEN SOAKED IN MOTHER LIQUOR CONTAINING 0.2M MNCL2 AND 50 mM OXALOACETATE (the substrate) FOR 15 min, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution: 1.65→19.92 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.21 / Isotropic thermal model: Isotropic / σ(F): 1.48 / Phase error: 17.8 / Stereochemistry target values: ML Details: ANISOTROPIC B VALUES DERIVED FROM FROM TLS REFINEMENT, HYDROGENS ARE INCLUDED AS RIDING MODEL
Rfactor
Num. reflection
% reflection
Rfree
0.201
1552
5.09 %
Rwork
0.172
-
-
obs
0.174
30472
99.9 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.99 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Biso mean: 21.98 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.327 Å2
-0 Å2
0 Å2
2-
-
-0.327 Å2
-0 Å2
3-
-
-
0.465 Å2
Refinement step
Cycle: LAST / Resolution: 1.65→19.92 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2179
0
8
306
2493
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
4392
X-RAY DIFFRACTION
f_angle_d
0.862
7937
X-RAY DIFFRACTION
f_dihedral_angle_d
16
1110
X-RAY DIFFRACTION
f_chiral_restr
0.062
344
X-RAY DIFFRACTION
f_plane_restr
0.003
682
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.65-1.703
0.306
141
0.295
2565
X-RAY DIFFRACTION
100
1.703-1.764
0.338
132
0.263
2592
X-RAY DIFFRACTION
100
1.764-1.835
0.284
143
0.235
2580
X-RAY DIFFRACTION
100
1.835-1.918
0.263
143
0.21
2589
X-RAY DIFFRACTION
100
1.918-2.019
0.201
126
0.169
2603
X-RAY DIFFRACTION
100
2.019-2.146
0.178
131
0.146
2622
X-RAY DIFFRACTION
100
2.146-2.311
0.204
144
0.152
2592
X-RAY DIFFRACTION
100
2.311-2.543
0.175
148
0.142
2633
X-RAY DIFFRACTION
100
2.543-2.91
0.143
147
0.139
2647
X-RAY DIFFRACTION
100
2.91-3.663
0.186
134
0.143
2693
X-RAY DIFFRACTION
100
3.663-19.921
0.181
163
0.175
2804
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.3331
0.042
0.0662
0.7102
-0.3601
0.4552
-0.0168
0.0156
-0.0117
0.1053
-0.0127
-0.0959
-0.0382
0.0443
0
0.0687
-0.0024
-0.024
0.053
0.01
0.0669
18.5004
2.1706
-25.8393
2
0.1134
-0.1328
0.022
0.2482
-0.0335
0.0976
-0.0279
0.0274
0.0416
0.0591
0.0271
-0.1095
-0.0226
0.0168
0.0623
0.0276
-0.0071
-0.0264
0.0019
-0.0091
0.0221
19.3107
1.1533
-25.8754
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN A AND RESIDUE 68-361
2
X-RAY DIFFRACTION
2
NOT (CHAIN A AND RESIDUE 68-361)
+
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