- PDB-6r3z: Structure of the SBP FpvC in complex with Ni2+ ion from P. aerugi... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6r3z
Title
Structure of the SBP FpvC in complex with Ni2+ ion from P. aeruginosa in P212121 space group
Components
Probable adhesion protein
Keywords
TRANSPORT PROTEIN / solute binding protein (transport system)
Function / homology
Adhesin B / metal ion transport / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / cell adhesion / metal ion binding / NICKEL (II) ION / Probable adhesion protein
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97 Å / Relative weight: 1
Reflection
Resolution: 1.65→39.26 Å / Num. obs: 30063 / % possible obs: 97.8 % / Redundancy: 10 % / Biso Wilson estimate: 27.93 Å2 / Rpim(I) all: 0.051 / Rsym value: 0.11 / Net I/σ(I): 12.8
Reflection shell
Resolution: 1.65→1.75 Å / Num. unique obs: 4251
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Processing
Software
Name
Version
Classification
BUSTER
2.10.3
refinement
XDS
datareduction
XSCALE
datascaling
FFT
phasing
Refinement
Method to determine structure: FOURIER SYNTHESIS Starting model: model soved by SAD Resolution: 1.65→39.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.102
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.219
1504
5 %
RANDOM
Rwork
0.184
-
-
-
obs
0.186
30063
98 %
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Displacement parameters
Biso mean: 32 Å2
Baniso -1
Baniso -2
Baniso -3
1-
9.1488 Å2
0 Å2
0 Å2
2-
-
-9.192 Å2
0 Å2
3-
-
-
0.0432 Å2
Refine analyze
Luzzati coordinate error obs: 0.23 Å
Refinement step
Cycle: 1 / Resolution: 1.65→39.26 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2065
0
29
255
2349
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2138
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.97
2888
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
742
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
X-RAY DIFFRACTION
t_gen_planes
358
HARMONIC
5
X-RAY DIFFRACTION
t_it
2138
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.23
X-RAY DIFFRACTION
t_other_torsion
15.94
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
284
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
2669
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.65→1.66 Å / Total num. of bins used: 50
Rfactor
Num. reflection
% reflection
Rfree
0.4255
-
4.98 %
Rwork
0.3199
572
-
all
0.3244
602
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obs
-
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76.43 %
Refinement TLS params.
Method: refined / Origin x: -17.5627 Å / Origin y: -2.3093 Å / Origin z: 11.0395 Å
11
12
13
21
22
23
31
32
33
T
-0.0142 Å2
0.005 Å2
-0.0055 Å2
-
0.0116 Å2
0.0128 Å2
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-
-0.0183 Å2
L
0.5679 °2
0.0627 °2
-0.0503 °2
-
0.7999 °2
-0.2322 °2
-
-
0.344 °2
S
0.0075 Å °
-0.0105 Å °
0.0016 Å °
-0.0562 Å °
0 Å °
-0.023 Å °
0.0413 Å °
0.02 Å °
-0.0075 Å °
Refinement TLS group
Selection details: { A|41 - A|130 A|142 - A|316 }
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