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148969
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1GKK
Feruloyl esterase domain of XynY from clostridium thermocellum
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 1 (gz) (A+S)
Biological Assembly 2 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
pH
7.5
Details
HEPES PH 7.5 100MM, NA ACETATE 1M, CD ACETATE 50 MM, GLYCEROL 5%
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 65.38
α = 90
b = 108.79
β = 90
c = 113.88
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
120
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 4
CYLINDRICAL GRAZING INCIDENCE MIRROR
2000-12-15
Diffraction Radiation
Monochromator
Protocol
SI
MAD
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID29
0.9754,0.9796
ESRF
ID29
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
1.6
30
99.1
0.055
--
--
3.9
--
106584
--
--
--
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)
1.6
1.69
95.1
0.224
--
3.0
2.9
--
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
MAD
1.6
20.0
--
--
--
101173
5323
99.0
--
0.155
0.154
0.173
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
1.6
1.64
--
362
6890
0.195
0.21
--
--
RMS Deviations
Key
Refinement Restraint Deviation
r_chiral_restr
0.108
r_symmetry_hbond_refined
0.179
r_angle_other_deg
1.576
r_scbond_it
2.337
r_dihedral_angle_3_deg
2.801
r_mcbond_it
0.919
r_bond_refined_d
0.016
r_bond_other_d
0.003
r_gen_planes_refined
0.009
r_symmetry_vdw_other
0.236
r_xyhbond_nbd_refined
0.136
r_symmetry_vdw_refined
0.288
r_metal_ion_refined
0.173
r_nbd_refined
0.224
r_nbtor_other
0.323
r_gen_planes_other
0.006
r_scangle_it
3.476
r_mcangle_it
1.511
r_nbd_other
0.197
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
4574
Nucleic Acid Atoms
0
Heterogen Atoms
16
Solvent Atoms
751
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.0
MOSFLM
data reduction
SCALA
data scaling
TRUNCATE
data scaling
SOLVE
phasing