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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1EAV
Crystal Structures of Human Gephyrin and Plant Cnx1 G domains - Comparative Analysis and Functional Implications
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)
Biological Assembly 3 (gz) (A+S)
Biological Assembly 4 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
pH
6.5
Details
1.4 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE, PH 6.5
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 175.3
α = 90
b = 175.3
β = 90
c = 175.3
γ = 90
Symmetry
Space Group
P 21 3
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
MARRESEARCH
PLANAR MIRROR AND TOROIDAL MIRROR
2000-05-15
Diffraction Radiation
Monochromator
Protocol
SI(111)
MAD
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
MPG/DESY, HAMBURG BEAMLINE BW6
0.9790, 0.97940, 0.9500, 1.0448
MPG/DESY, HAMBURG
BW6
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
2.6
27
90.8
0.062
--
--
2.7
--
47553
--
--
--
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)
2.6
2.74
75.5
0.159
--
4.3
1.7
--
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
2.6
27.0
--
--
--
47553
2582
90.8
--
--
0.223
0.251
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
2.6
2.67
--
140
2834
0.33
0.388
--
--
RMS Deviations
Key
Refinement Restraint Deviation
r_chiral_restr
0.131
r_xyhbond_nbd_refined
0.158
r_mcbond_it
1.272
r_mcangle_it
2.403
r_symmetry_vdw_refined
0.345
r_bond_other_d
0.002
r_gen_planes_refined
0.008
r_bond_refined_d
0.032
r_angle_other_deg
2.499
r_symmetry_vdw_other
0.285
r_dihedral_angle_3_deg
1.112
r_scangle_it
6.403
r_gen_planes_other
0.004
r_nbd_other
0.25
r_nbd_refined
0.282
r_symmetry_hbond_refined
0.178
r_scbond_it
3.655
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
9450
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
51
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.0.36
MOSFLM
data reduction
SCALA
data scaling
SOLVE
phasing