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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
1JYJ
Crystal Structure of a Double Variant (W67L/W91H) of Recombinant Human Serum Retinol-binding Protein at 2.0 A Resolution
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)
Biological Assembly (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
9.1
Temperature
289.0
Details
Sodium Chloride, Tris/HCl buffer, beta-octyl-glucoside, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 102.76
α = 90
b = 102.76
β = 90
c = 72.72
γ = 120
Symmetry
Space Group
H 3
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MARRESEARCH
--
--
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X31
1.09
EMBL/DESY, Hamburg
X31
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
40
98.0
--
0.102
--
5.8
--
18890
0.0
0.0
18.8
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)
2.0
2.07
92.7
--
0.37
3.19
--
1798
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
2.0
19.66
0.0
0.0
18890
18890
900
97.8
--
0.209
0.205
0.229
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
2.0
2.13
--
137
2851
0.244
0.269
0.023
93.6
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
RESTRAINED
Mean Isotropic B
22.4
Anisotropic B[1][1]
0.94
Anisotropic B[1][2]
1.44
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.94
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-1.89
RMS Deviations
Key
Refinement Restraint Deviation
c_angle_deg
1.4
c_improper_angle_d
0.69
c_bond_d
0.006
c_dihedral_angle_d
24.7
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.23
Luzzati Sigma A (Observed)
0.19
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.26
Luzzati Sigma A (R-Free Set)
0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1397
Nucleic Acid Atoms
0
Heterogen Atoms
30
Solvent Atoms
218
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
AMoRE
phasing
CNS
refinement version: 1.0