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
Nov 16, 2021
Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0
Nov 16, 2022
Provider: repository / Type: Initial release
Revision 1.1
May 29, 2024
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.2→50 Å / Num. obs: 318404 / % possible obs: 97.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.573 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 33
Reflection shell
Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.42 / Num. unique obs: 30785
-
Processing
Software
Name
Version
Classification
REFMAC
5.5.0110
refinement
HKL-2000
datareduction
HKL-2000
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MIR / Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.481 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.16916
16069
5 %
RANDOM
Rwork
0.15712
-
-
-
obs
0.15772
302246
97.49 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK