Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection
Resolution: 2.4→46.5 Å / Num. all: 23686 / Num. obs: 23686 / % possible obs: 99.5 %
Reflection shell
Resolution: 2.4→2.53 Å / % possible all: 97.3
-
Processing
Software
Name
Version
Classification
EDNA
datacollection
MOLREP
phasing
REFMAC
5.6.0117
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: native PgaE Resolution: 2.4→46.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.922 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25927
1216
5.1 %
RANDOM 5 %
Rwork
0.19847
-
-
-
obs
0.2015
22469
99.42 %
-
all
-
23686
-
-
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: 58.552 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.91 Å2
-0 Å2
0 Å2
2-
-
-3.63 Å2
0 Å2
3-
-
-
2.71 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→46.5 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3469
0
93
113
3675
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.019
3609
X-RAY DIFFRACTION
r_angle_refined_deg
1.341
1.978
4901
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.584
5
465
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.788
22.81
153
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.517
15
546
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.503
15
34
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
543
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2747
LS refinement shell
Resolution: 2.4→2.462 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.314
80
-
Rwork
0.305
1513
-
obs
-
-
95.33 %
Refinement TLS params.
Method: refined / Origin x: 28.831 Å / Origin y: 25.3657 Å / Origin z: 26.5758 Å
11
12
13
21
22
23
31
32
33
T
0.0179 Å2
0.0054 Å2
0.0169 Å2
-
0.0154 Å2
-0.008 Å2
-
-
0.0515 Å2
L
0.1274 °2
-0.164 °2
0.1368 °2
-
0.8022 °2
0.1423 °2
-
-
0.3229 °2
S
0.0257 Å °
-0.021 Å °
0.0286 Å °
-0.1136 Å °
-0.0195 Å °
-0.1258 Å °
-0.0154 Å °
-0.0491 Å °
-0.0061 Å °
+
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