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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
1YXV
Crystal Structure of Kinase Pim1 in complex with 3,4-Dihydroxy-1-methylquinolin-2(1H)-one
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)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop
pH
6.5
Temperature
277.0
Details
Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 96.59
α = 90
b = 96.59
β = 90
c = 80.56
γ = 120
Symmetry
Space Group
P 65
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 4
--
2002-02-22
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ALS BEAMLINE 8.3.1
--
ALS
8.3.1
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
84.57
99.7
0.065
0.065
--
4.0
29618
29538
1.5
1.5
--
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
2.05
99.2
0.758
0.758
0.8
3.5
--
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
84.51
--
1.5
29618
27964
1495
99.47
0.189
0.188
0.188
0.211
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
2.052
--
111
2025
0.289
0.308
--
--
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
22.693
Anisotropic B[1][1]
0.95
Anisotropic B[1][2]
0.48
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.95
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-1.43
RMS Deviations
Key
Refinement Restraint Deviation
r_symmetry_hbond_refined
0.115
r_mcbond_it
0.583
r_nbd_other
0.232
r_mcangle_it
1.103
r_scbond_it
1.45
r_symmetry_vdw_refined
0.135
r_bond_refined_d
0.009
r_bond_other_d
0.002
r_nbtor_other
0.079
r_chiral_restr
0.084
r_angle_refined_deg
1.255
r_nbd_refined
0.198
r_gen_planes_other
0.004
r_angle_other_deg
0.8
r_xyhbond_nbd_refined
0.156
r_dihedral_angle_1_deg
2.915
r_scangle_it
2.467
r_gen_planes_refined
0.005
r_symmetry_vdw_other
0.267
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2230
Nucleic Acid Atoms
0
Heterogen Atoms
19
Solvent Atoms
170
Software
Software
Software Name
Purpose
SCALA
data scaling
REFMAC
refinement version: 5.1.25
PDB_EXTRACT
data extraction version: 1.600
MOSFLM
data reduction
CCP4
data scaling version: (SCALA)
MOLREP
phasing