- PDB-3mvn: Crystal structure of a domain from a putative UDP-N-acetylmuramat... -
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Basic information
Entry
Database: PDB / ID: 3mvn
Title
Crystal structure of a domain from a putative UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase from Haemophilus ducreyi 35000HP
Resolution: 1.9→1.93 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 7.1 / Rsym value: 0.446 / % possible all: 100
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Processing
Software
Name
Version
Classification
Blu-Ice
Max
datacollection
HKL-3000
phasing
MLPHARE
phasing
DM
modelbuilding
SHELXD
phasing
ARP/wARP
modelbuilding
Coot
modelbuilding
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
DM
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.9→20.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.451 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.662 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23707
479
4.8 %
RANDOM
Rwork
0.1588
-
-
-
obs
0.1622
9464
99.21 %
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all
-
9943
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 23.008 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refine analyze
Luzzati coordinate error obs: 0.2 Å
Refinement step
Cycle: LAST / Resolution: 1.9→20.62 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
950
0
0
67
1017
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
974
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
626
X-RAY DIFFRACTION
r_angle_refined_deg
1.412
1.948
1325
X-RAY DIFFRACTION
r_angle_other_deg
0.956
3
1543
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.707
5
122
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
44.096
25.333
45
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.194
15
165
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.132
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
160
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1077
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
175
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.45
1.5
618
X-RAY DIFFRACTION
r_mcbond_other
0.442
1.5
247
X-RAY DIFFRACTION
r_mcangle_it
2.313
2
998
X-RAY DIFFRACTION
r_scbond_it
3.812
3
356
X-RAY DIFFRACTION
r_scangle_it
5.915
4.5
327
X-RAY DIFFRACTION
r_rigid_bond_restr
1.766
3
1600
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.899→1.947 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.217
42
-
Rwork
0.156
684
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 22.4794 Å / Origin y: 4.2322 Å / Origin z: 37.2982 Å
11
12
13
21
22
23
31
32
33
T
0.0165 Å2
-0.001 Å2
0.005 Å2
-
0.0547 Å2
-0.0073 Å2
-
-
0.06 Å2
L
1.4673 °2
-0.0941 °2
-0.2741 °2
-
1.2952 °2
-0.1121 °2
-
-
1.5154 °2
S
0.0064 Å °
0.0385 Å °
-0.0724 Å °
-0.0736 Å °
0.0017 Å °
0.004 Å °
0.134 Å °
-0.0422 Å °
-0.0081 Å °
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