5DWR

Identification of N-(4-((1R,3S,5S)-3-amino-5-methylcyclohexyl)pyridin-3-yl)-6-(2,6-difluorophenyl)-5-fluoropicolinamide (PIM447), a Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (PIM) 1,2 and 3 Kinase Inhibitor in Clinical Trials for Hematological Malignancies


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details Crystallant: 0.6 to 1.0 mM Ammonium monophosphate (NH4)2HPO4, 200-350 mM sodium chloride, 0.1 M Citrate, pH 5.5, 1ul (10mg/ml) protein : 1ul crystallant

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.23 α = 90
b = 98.23 β = 90
c = 81.12 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 160
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-05-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.9765 ALS 5.0.1

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 42.59 100.0 0.194 -- -- 6.1 -- 30274 -- -- 28.76
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 2.11 100.0 0.436 -- 3.3 6.2 --

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
-- 2.0 25.44 -- 0.0 -- 30094 1525 99.97 -- 0.1748 0.1734 0.2022 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 2.07 -- 156 2770 0.1794 0.2088 -- 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.66
Anisotropic B[1][1] -0.3289
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3289
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.6578
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 17.42
t_omega_torsion 3.11
t_angle_deg 0.96
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.198
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2214
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 248

Software

Software
Software Name Purpose
BUSTER refinement version: 2.11.4
MOSFLM data reduction
SCALA data scaling
MOLREP phasing