Resolution: 2.4→54.554 Å / Num. all: 18532 / Num. obs: 18532 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13
Reflection shell
Resolution: 2.4→2.46 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1325 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 41.97 Å / Num. measured all: 94513
Reflection shell
*PLUS
% possible obs: 98.8 %
-
Processing
Software
Name
Version
Classification
MOSFLM
datareduction
SCALA
datascaling
SOLVE
phasing
RESOLVE
modelbuilding
REFMAC
5.1.9999
refinement
CCP4
(SCALA)
datascaling
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.4→41.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.449 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.215 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. SELENIUM OCCUPANCIES WERE SET TO 0.5, TO REFLECT VARIABLE INCORPORATION DURING EXPRESSION. THIS VALUE MINIMIZES RFREE AND THE AMOUNT OF DIFFERENCE DENSITY OVER THE SITES. 2. RESIDUES 188- ...Details: 1. SELENIUM OCCUPANCIES WERE SET TO 0.5, TO REFLECT VARIABLE INCORPORATION DURING EXPRESSION. THIS VALUE MINIMIZES RFREE AND THE AMOUNT OF DIFFERENCE DENSITY OVER THE SITES. 2. RESIDUES 188-193 WERE OMITTED, BECAUSE THE STRONG DIFFERENCE DENSITY REMAINED AMBIGUOUS ABOUT THE PATH OF MAIN CHAIN TRACE; THE DENSITY WAS MODELED WITH WATER. 3. THE N-TERMINUS RETAINS STRONG DIFFERENCE DENSITY, SUGGESTING A DOUBLE CONFORMATION FOR MSE1; THIS PROVED DIFFICULT TO MODEL, SO THE CONFORMATION AGREEING BEST WITH EXPERIMENTAL DENSITY WAS RETAINED. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22238
830
4.5 %
RANDOM
Rwork
0.17542
-
-
-
obs
0.17765
17676
99.77 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 57.277 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.4 Å2
-1.2 Å2
0 Å2
2-
-
-2.4 Å2
0 Å2
3-
-
-
3.61 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→41.97 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2548
0
0
218
2766
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2633
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2362
X-RAY DIFFRACTION
r_angle_refined_deg
1.505
1.913
3554
X-RAY DIFFRACTION
r_angle_other_deg
0.832
3
5478
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.304
5
312
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.267
23.206
131
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.738
15
446
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.963
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
372
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2920
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
579
X-RAY DIFFRACTION
r_nbd_refined
0.185
0.2
479
X-RAY DIFFRACTION
r_nbd_other
0.199
0.2
2422
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
1648
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.022
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.148
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.302
0.2
46
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.164
0.2
20
X-RAY DIFFRACTION
r_mcbond_it
0.832
1.5
1672
X-RAY DIFFRACTION
r_mcangle_it
1.285
2
2531
X-RAY DIFFRACTION
r_scbond_it
1.706
3
1201
X-RAY DIFFRACTION
r_scangle_it
2.603
4.5
1023
LS refinement shell
Resolution: 2.4→2.462 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rwork
0.245
1323
Rfree
-
0
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
3.3975
1.3062
-0.5912
2.0648
-0.6154
1.9452
0.0171
-0.3583
0.4264
0.3071
-0.1626
0.3068
-0.1779
-0.0122
0.1455
-0.243
0.0106
0.027
-0.2104
-0.093
-0.2905
31.823
53.282
49.019
2
3.0547
-0.3312
-0.974
4.775
-0.7944
3.0036
-0.0425
-0.1506
0.0814
0.1398
0.1777
0.7001
0.073
-0.0168
-0.1352
-0.3778
0.0183
0.0501
-0.2744
-0.0211
-0.3478
15.881
29.324
46.217
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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