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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
4HCZ
PHF1 Tudor in complex with H3K36me3
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
Method
Vapor Diffusion Sitting Drop
pH
7.5
Temperature
277.15
Details
0.1 M HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 88.03
α = 90
b = 29.67
β = 116.41
c = 62
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
RIGAKU RAXIS IV++
--
2011-01-20
Diffraction Radiation
Monochromator
Protocol
Ni Filter
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU RUH3R
1.541
--
--
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
1.85
23.41
96.4
--
--
--
--
12091
12091
0.0
-3.0
25.16
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)
1.85
1.92
81.1
--
--
--
--
--
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
1.85
23.413
--
0.0
12091
12073
580
96.23
--
0.2058
0.2038
0.2439
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
1.85
2.0361
--
144
2667
0.2898
0.3932
--
91.0
X Ray Diffraction
2.0361
2.3305
--
156
2932
0.2061
0.2511
--
99.0
X Ray Diffraction
2.3305
2.9353
--
129
2977
0.2031
0.2705
--
99.0
X Ray Diffraction
2.9353
23.4144
--
151
2917
0.1886
0.2066
--
95.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
30.1275
Anisotropic B[1][1]
-3.3304
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-1.231
Anisotropic B[2][2]
-5.0827
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
8.413
RMS Deviations
Key
Refinement Restraint Deviation
f_bond_d
0.007
f_angle_d
1.06
f_chiral_restr
0.071
f_dihedral_angle_d
14.919
f_plane_restr
0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1061
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
161
Software
Software
Software Name
Purpose
PHASER
phasing
PHENIX
refinement version: 1.6.4_486
PDB_EXTRACT
data extraction version: 3.11
CrystalClear
data collection
d*TREK
data reduction
d*TREK
data scaling