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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
3ERQ
Crystal structure of Staphylococcal nuclease variant L25K at cryogenic temperature
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
8
Temperature
277.0
Details
22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, Soaked in higher % MPD before freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 30.98
α = 90
b = 60.28
β = 93.43
c = 37.96
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
110
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
BRUKER APEX II
multi-layer optics
2008-06-15
Diffraction Radiation
Monochromator
Protocol
GE111
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SEALED TUBE
OTHER
1.5418
--
--
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
2.1
60.28
100.0
0.0816
0.0349
--
15.45
8220
8216
0.0
0.0
38.6
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)
2.1
2.2
100.0
0.388
0.2114
4.49
11.86
1058
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
2.1
23.29
--
0.0
8181
8181
803
99.78
0.215
0.215
0.209
0.278
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
2.1
2.154
585
60
521
0.303
0.365
--
99.316
X Ray Diffraction
2.154
2.213
600
67
--
0.247
0.35
--
99.5
X Ray Diffraction
2.216
2.276
548
61
--
0.244
0.327
--
99.635
X Ray Diffraction
2.276
2.346
563
65
--
0.243
0.354
--
99.467
X Ray Diffraction
2.346
2.422
527
53
--
0.249
0.384
--
100.0
X Ray Diffraction
2.422
2.506
529
46
--
0.249
0.338
--
99.811
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
31.224
Anisotropic B[1][1]
-0.05
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.01
Anisotropic B[2][2]
0.01
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
0.04
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_3_deg
17.072
r_gen_planes_refined
0.008
r_bond_refined_d
0.008
r_mcbond_it
0.934
r_chiral_restr
0.095
r_angle_refined_deg
1.216
r_dihedral_angle_2_deg
33.39
r_dihedral_angle_4_deg
14.772
r_scangle_it
3.985
r_dihedral_angle_1_deg
7.064
r_mcangle_it
1.683
r_scbond_it
2.636
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1034
Nucleic Acid Atoms
0
Heterogen Atoms
26
Solvent Atoms
45
Software
Software
Software Name
Purpose
SAINT
data scaling
PHASER
phasing
REFMAC
refinement version: 5.5.0036
PDB_EXTRACT
data extraction version: 3.006
APEX
data collection
SAINT
data reduction