Ministry of Education, Culture, Sports, Science and Technology (Japan)
24780106
Japan
Citation
Journal: To Be Published Title: Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5 Authors: Nakajima, Y.
History
Deposition
Sep 29, 2021
Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0
Oct 5, 2022
Provider: repository / Type: Initial release
Revision 1.1
Oct 12, 2022
Group: Structure summary / Category: audit_author
Revision 1.2
May 29, 2024
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2015
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.58→50 Å / Num. obs: 76668 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 57.5
Reflection shell
Resolution: 1.58→1.64 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 15.9 / Num. unique obs: 7559 / CC1/2: 0.994 / CC star: 0.999 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0103
refinement
HKL-2000
datareduction
HKL-2000
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MIR / Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.154 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18266
3739
4.9 %
RANDOM
Rwork
0.15003
-
-
-
obs
0.15159
72749
99.84 %
-
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