- PDB-2qq6: Crystal structure of mandelate racemase/muconate lactonizing enzy... -
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Basic information
Entry
Database: PDB / ID: 2qq6
Title
Crystal structure of mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus DSM 9941
Components
Mandelate racemase/muconate lactonizing enzyme-like protein
Keywords
ISOMERASE / enolase / Mg ion / 9367a / PSI-2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Resolution: 2.9→3 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.593 / % possible all: 98.2
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Processing
Software
Name
Version
Classification
CBASS
datacollection
SOLVE
phasing
SHARP
phasing
CNS
1.1
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2823
829
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RANDOM
Rwork
0.2218
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-
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all
0.257
22830
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obs
0.2218
21554
94.4 %
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Solvent computation
Bsol: 0.332041 Å2
Displacement parameters
Biso mean: 48.7385 Å2
Baniso -1
Baniso -2
Baniso -3
1-
13.971 Å2
0 Å2
0 Å2
2-
-
13.971 Å2
0 Å2
3-
-
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-27.941 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.5 Å
0.37 Å
Luzzati sigma a
0.61 Å
0.54 Å
Refinement step
Cycle: LAST / Resolution: 2.9→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6021
0
2
28
6051
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.009
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.5
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
X-RAY DIFFRACTION
c_mcangle_it
X-RAY DIFFRACTION
c_scbond_it
X-RAY DIFFRACTION
c_scangle_it
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