#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43 Authors: Nonaka, T. / Fujihashi, M. / Kita, A. / Saeki, K. / Ito, S. / Miki, K.
History
Deposition
Jul 8, 2004
Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0
Sep 14, 2004
Provider: repository / Type: Initial release
Revision 1.1
Apr 30, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Source and taxonomy / Version format compliance
Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.85 Å / Relative weight: 1
Reflection
Resolution: 1.3→100 Å / Num. obs: 94791 / % possible obs: 98 % / Redundancy: 4.799 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.761
Reflection shell
Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.091 / % possible all: 98.5
-
Processing
Software
Name
Classification
SHELX
modelbuilding
SHELXL-97
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
CNS
phasing
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→100 Å / Num. parameters: 34075 / Num. restraintsaints: 42340 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Water molecules from HOH 3458 to 3461 are related to multi-conformational ASN A 1. Water molecule HOH 4446 is related to multi-conformational ASN A 153.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1691
4720
-
RANDOM
obs
0.134
89716
92.6 %
-
all
-
94436
-
-
Refine analyze
Num. disordered residues: 23 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3666.63
Refinement step
Cycle: LAST / Resolution: 1.3→100 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3194
0
32
458
3684
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
s_bond_d
0.015
X-RAY DIFFRACTION
s_angle_d
0.029
X-RAY DIFFRACTION
s_similar_dist
0.009
X-RAY DIFFRACTION
s_from_restr_planes
0.0303
X-RAY DIFFRACTION
s_zero_chiral_vol
0.071
X-RAY DIFFRACTION
s_non_zero_chiral_vol
0.073
X-RAY DIFFRACTION
s_anti_bump_dis_restr
0.025
X-RAY DIFFRACTION
s_rigid_bond_adp_cmpnt
0.004
X-RAY DIFFRACTION
s_similar_adp_cmpnt
0.03
X-RAY DIFFRACTION
s_approx_iso_adps
0.076
+
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