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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
4KHU
Ternary complex of rb69 mutant L415F with a ribonucleotide at -1 position
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+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop
pH
7
Temperature
298.0
Details
50 MM TRIS-HCL, 13% PEG350, 180 MM CALCIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 80.98
α = 90
b = 119.35
β = 90
c = 127.86
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
95
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MAR scanner 300 mm plate
--
2010-05-12
Diffraction Radiation
Monochromator
Protocol
MIRRORS
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU MICROMAX-007 HF
--
--
--
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
2.05
50
97.9
0.089
--
--
--
64642
64642
0.0
2.6
--
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)
2.05
2.12
84.0
0.503
--
--
--
--
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
2.05
21.62
--
0.0
64642
64642
3199
82.8
--
0.209
0.207
0.247
--
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
2.052
2.0825
--
107
2181
0.2865
0.4009
--
69.0
X Ray Diffraction
2.0825
2.115
--
135
2448
0.2747
0.3562
--
77.0
X Ray Diffraction
2.115
2.1497
--
140
2636
0.258
0.3098
--
83.0
X Ray Diffraction
2.1497
2.1867
--
126
2799
0.2321
0.3072
--
86.0
X Ray Diffraction
2.1867
2.2265
--
133
2756
0.219
0.2454
--
87.0
X Ray Diffraction
2.2265
2.2692
--
140
2753
0.2269
0.3393
--
86.0
X Ray Diffraction
2.2692
2.3155
--
123
2434
0.258
0.2891
--
76.0
X Ray Diffraction
2.3155
2.3658
--
136
2475
0.2578
0.3713
--
78.0
X Ray Diffraction
2.3658
2.4207
--
119
2319
0.2542
0.3058
--
73.0
X Ray Diffraction
2.4207
2.4812
--
127
2297
0.275
0.3496
--
72.0
X Ray Diffraction
2.4812
2.5482
--
113
2357
0.2627
0.2977
--
73.0
X Ray Diffraction
2.5482
2.623
--
140
2345
0.2767
0.3105
--
74.0
X Ray Diffraction
2.623
2.7076
--
141
2353
0.258
0.303
--
74.0
X Ray Diffraction
2.7076
2.8041
--
123
2344
0.2745
0.2987
--
73.0
X Ray Diffraction
2.8041
2.9161
--
120
2435
0.2567
0.2829
--
75.0
X Ray Diffraction
2.9161
3.0485
--
128
2537
0.2347
0.2731
--
79.0
X Ray Diffraction
3.0485
3.2088
--
136
2855
0.2196
0.2841
--
88.0
X Ray Diffraction
3.2088
3.4091
--
170
3133
0.206
0.217
--
97.0
X Ray Diffraction
3.4091
3.6711
--
169
3233
0.1981
0.2257
--
99.0
X Ray Diffraction
3.6711
4.0384
--
158
3110
0.1687
0.2051
--
95.0
X Ray Diffraction
4.0384
4.6178
--
176
3038
0.135
0.1769
--
93.0
X Ray Diffraction
4.6178
5.7993
--
180
3189
0.1467
0.1807
--
96.0
X Ray Diffraction
5.7993
21.622
--
159
3416
0.2138
0.252
--
99.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
-0.4673
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
-5.0015
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
5.4688
RMS Deviations
Key
Refinement Restraint Deviation
f_angle_d
1.209
f_plane_restr
0.005
f_bond_d
0.013
f_dihedral_angle_d
12.897
f_chiral_restr
0.074
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
7217
Nucleic Acid Atoms
651
Heterogen Atoms
36
Solvent Atoms
553
Software
Software
Software Name
Purpose
PHENIX
model building version: (PHENIX.REFINE: 1.7_650)
PHENIX
refinement version: (PHENIX.REFINE: 1.7_650)
HKL-2000
data reduction
HKL-2000
data scaling
PHENIX
phasing version: 1.7_650