Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Sequence details
5XHIS TAG AT THE C-TERMINUS WAS DESIGNED, BUT IT SEEMS TO BE AUTO-CLEAVED BY THE PROTEASE IN THE ...5XHIS TAG AT THE C-TERMINUS WAS DESIGNED, BUT IT SEEMS TO BE AUTO-CLEAVED BY THE PROTEASE IN THE CRYSTAL, JUDGED BY THE ELECTRON DENSITY AT 1.5 A RESOLUTION (FROM THE FREE ENZYME).
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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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal grow
Temperature: 293 K / Method: vapor diffusion / pH: 6.9 Details: VAPOR DIFFUSION AT 20C, 6% W/V POLYETHYLENE GLYCOL 3350, 2% V/V TACSIMATE, 5% V/V 2-PROPANOL, 0.1 M IMIDAZOLE PH 6.9; THEN THE CRYSTAL WAS SOAKED IN THE MOTHER LIQUOR SUPPLEMENTED WITH 2MM ...Details: VAPOR DIFFUSION AT 20C, 6% W/V POLYETHYLENE GLYCOL 3350, 2% V/V TACSIMATE, 5% V/V 2-PROPANOL, 0.1 M IMIDAZOLE PH 6.9; THEN THE CRYSTAL WAS SOAKED IN THE MOTHER LIQUOR SUPPLEMENTED WITH 2MM SG85 FOR 48H, TO GET THE COMPLEX CRYSTAL.
Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91841 Å / Relative weight: 1
Reflection
Resolution: 1.96→178.67 Å / Num. obs: 47447 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 29.82 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.9
Reflection shell
Resolution: 1.96→2 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9
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Processing
Software
Name
Version
Classification
BUSTER
2.11.2
refinement
AutoPROC
datareduction
XDS
datareduction
AutoPROC
datascaling
XDS
datascaling
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→68.72 Å / Cor.coef. Fo:Fc: 0.9541 / Cor.coef. Fo:Fc free: 0.9416 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.128 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9812. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9812. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=5. GERNERALLY MAIN CHAIN ATOMS ARE MODELED BASED ON CLEAR ELECTRON DENSITY.HOWEVER,SOME RESIDUES IN THE LOOP REGION, WHICH SHOW SMALL GAP IN ELECTRON DENSITY, ARE MODELED STEREOCHEMICALLY. SIDE CHAIN ATOMS ARE MODELED BASED ON EITHER CLEAR ELECTRON DENSITY, OR STEREOCHEMICALLY WHEN THE ELECTRON DENSITY IS NOT DEFINED BUT THE MAIN CHAIN ATOMS OF THAT RESIDUE ARE MODELED. THE RESTRAINTS FOR SG85 AND ITS LINK TO PROTEIN WERE GENERATED BY GRADE WEBSEVER (GLOBAL PHASING LTD.)
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1979
2370
5 %
RANDOM
Rwork
0.1714
-
-
-
obs
0.1727
47400
99.48 %
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Displacement parameters
Biso mean: 35.67 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.8022 Å2
0 Å2
0 Å2
2-
-
-1.8022 Å2
0 Å2
3-
-
-
3.6045 Å2
Refine analyze
Luzzati coordinate error obs: 0.221 Å
Refinement step
Cycle: LAST / Resolution: 1.96→68.72 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4618
0
49
481
5148
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
9445
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.09
17027
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2049
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
111
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1476
HARMONIC
5
X-RAY DIFFRACTION
t_it
9445
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
1
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.93
X-RAY DIFFRACTION
t_other_torsion
14.88
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
645
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
10585
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.96→2.01 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2217
163
5.04 %
Rwork
0.1841
3070
-
all
0.186
3233
-
obs
-
-
99.48 %
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
1.2154
0.0154
-0.6713
0.4683
0.0363
1.0866
0.0112
-0.0309
-0.0653
0.0769
-0.0387
-0.1023
0.0128
0.0835
0.0275
-0.0523
0.0601
0.0004
-0.0822
0.0209
-0.0971
17.1313
51.143
27.1805
2
1.5779
-0.8129
0.5126
1.3627
-0.3034
1.0586
-0.0093
-0.1146
-0.2033
-0.0287
0.0475
0.2784
0.0383
-0.2596
-0.0382
-0.1144
0.0325
0.0197
-0.0251
-0.0207
-0.0791
-3.9636
42.1809
14.9869
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
+
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