Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, MET 114 TO ARG ENGINEERED RESIDUE IN CHAIN B, MET 114 TO ARG
Sequence details
N-TERMINAL CLEAVABLE TAG LEAVES GSH AT N-TERMINUS. M102R MUTANT. PROTEIN CLONED FROM SECOND ...N-TERMINAL CLEAVABLE TAG LEAVES GSH AT N-TERMINUS. M102R MUTANT. PROTEIN CLONED FROM SECOND METHIONINE COMPARED WITH UNIPROT SEQUENCE.
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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: 3.64 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal grow
Temperature: 293 K / pH: 4.5 Details: 100 MM CITRATE/PHOSPHATE PH 4.5, 1 M AMMONIUM SULFATE AT 20 DEGREES C
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9806 Å / Relative weight: 1
Reflection
Resolution: 2.2→40 Å / Num. obs: 35308 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 35.95 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27
Reflection shell
Resolution: 2.2→2.27 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6 / % possible all: 99.5
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.2→40.748 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 22.33 / Stereochemistry target values: ML Details: PROTEIN WAS TREATED WITH TRYPSIN PRIOR TO CRYSTALLIZATION. CLIPPING MOST LIKELY AT ARG108.
Rfactor
Num. reflection
% reflection
Rfree
0.2222
1768
5 %
Rwork
0.1931
-
-
obs
0.1946
35308
95.99 %
Solvent computation
Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.017 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Biso mean: 40.5 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.394 Å2
0 Å2
0 Å2
2-
-
4.394 Å2
0 Å2
3-
-
-
-8.7879 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→40.748 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3269
0
10
190
3469
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
3374
X-RAY DIFFRACTION
f_angle_d
0.978
4541
X-RAY DIFFRACTION
f_dihedral_angle_d
13.135
1201
X-RAY DIFFRACTION
f_chiral_restr
0.069
482
X-RAY DIFFRACTION
f_plane_restr
0.003
598
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.1996-2.2783
0.3199
171
0.2429
3097
X-RAY DIFFRACTION
91
2.2783-2.3695
0.2797
171
0.2311
3165
X-RAY DIFFRACTION
92
2.3695-2.4773
0.2869
164
0.2149
3246
X-RAY DIFFRACTION
94
2.4773-2.6079
0.2343
158
0.2071
3291
X-RAY DIFFRACTION
95
2.6079-2.7712
0.2541
185
0.2058
3339
X-RAY DIFFRACTION
97
2.7712-2.9851
0.2353
188
0.2035
3379
X-RAY DIFFRACTION
98
2.9851-3.2854
0.234
164
0.2055
3451
X-RAY DIFFRACTION
99
3.2854-3.7605
0.2054
186
0.1834
3476
X-RAY DIFFRACTION
99
3.7605-4.7367
0.1743
199
0.1509
3442
X-RAY DIFFRACTION
98
4.7367-40.7555
0.2277
182
0.2078
3654
X-RAY DIFFRACTION
97
+
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