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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
1HWW
GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH SWAINSONINE
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)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
7
Temperature
298.0
Details
PEG 6000, MPD, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 68.9
α = 90
b = 110.01
β = 90
c = 138.47
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MARRESEARCH
Osmic focussing optics (mirrors)
2000-04-25
Diffraction Radiation
Monochromator
Protocol
Osmic mirrors
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU RU200
1.54189
--
--
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
1.87
69.24
99.7
0.078
--
--
6.9
87633
87633
0.0
0.0
13.8
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)
1.87
1.91
96.9
0.452
--
3.8
5.6
5601
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
1.87
69.24
1.0
1.0
87654
84829
4286
96.8
--
--
0.181
0.209
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
1.87
1.96
9907
506
9401
0.225
0.255
0.01
91.3
X Ray Diffraction
1.96
2.06
10383
509
9874
0.185
0.209
0.008
95.7
X Ray Diffraction
2.06
2.19
10442
497
9945
0.188
0.218
0.008
96.3
X Ray Diffraction
2.19
2.36
10578
543
10035
0.184
0.222
0.008
97.0
X Ray Diffraction
2.36
2.59
10633
560
10073
0.183
0.22
0.008
97.5
X Ray Diffraction
2.59
2.97
10762
543
10219
0.187
0.219
0.008
98.2
X Ray Diffraction
2.97
3.74
10914
542
10372
0.179
0.196
0.008
99.0
X Ray Diffraction
3.74
69.24
11210
586
10624
0.165
0.192
0.007
98.2
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
19.44
Anisotropic B[1][1]
-0.55
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.12
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
0.43
RMS Deviations
Key
Refinement Restraint Deviation
c_improper_angle_d
0.787
c_bond_d
0.005
c_dihedral_angle_d
24.19
c_angle_deg
1.3
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.18
Luzzati Sigma A (Observed)
0.11
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.21
Luzzati Sigma A (R-Free Set)
0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
8181
Nucleic Acid Atoms
0
Heterogen Atoms
35
Solvent Atoms
985
Software
Software
Software Name
Purpose
CNS
refinement version: 1.0
DENZO
data reduction
SCALEPACK
data scaling
CNS
phasing