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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1NX9
Acetobacter turbidans alpha-amino acid ester hydrolase S205A mutant complexed with ampicillin
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
5.6
Temperature
293.0
Details
PEG 4000, sodium citrate buffer, sodium ampicillin, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 341.83
α = 90
b = 341.83
β = 90
c = 341.83
γ = 90
Symmetry
Space Group
I 2 3
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MARRESEARCH
premirror, triangular monochromator, bent mirror
2002-11-18
Diffraction Radiation
Monochromator
Protocol
triangular
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE BW7B
0.8463
EMBL/DESY, Hamburg
BW7B
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
R Sym I (Observed)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
2.2
99
97.2
--
0.081
--
4.5
322911
322911
1.0
1.0
--
High Resolution Shell
Resolution (High)
Resolution (Low)
Percent Possible (All)
R Merge I (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
2.2
2.28
98.9
--
0.322
--
--
--
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
MOLECULAR REPLACEMENT
2.2
15.0
--
1.0
322911
304675
16078
96.9
0.16698
0.16618
0.16608
0.18386
RANDOM
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
2.2
2.256
--
1230
22491
0.21
0.234
--
--
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
22.609
RMS Deviations
Key
Refinement Restraint Deviation
r_bond_refined_d
0.007
r_nbd_refined
0.172
r_symmetry_vdw_refined
0.121
r_scbond_it
3.642
r_symmetry_hbond_refined
0.148
r_chiral_restr
0.075
r_mcbond_it
1.309
r_mcangle_it
2.212
r_scangle_it
5.286
r_gen_planes_refined
0.002
r_dihedral_angle_1_deg
2.21
r_angle_refined_deg
1.064
r_xyhbond_nbd_refined
0.101
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
19528
Nucleic Acid Atoms
0
Heterogen Atoms
120
Solvent Atoms
2229
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.1.19
DENZO
data reduction
SCALEPACK
data scaling
AMoRE
phasing