5AV2

Crystal structure of DAPK1-kaempferol complex in the presence of bromide ions.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 2 M ammonium sulfate, 0.1 M MES

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.83 α = 90
b = 62.33 β = 90
c = 88.38 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-11-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.91977 Photon Factory BL-5A

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
1.5 31.2 98.7 -- -- -- 7.5 -- 41406 -- -- --

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
-- 1.502 31.165 -- 1.51 -- 40112 2010 95.52 -- 0.1834 0.182 0.2088 --
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 1.5022 1.5397 -- 127 2396 0.3123 0.2966 -- 86.0
X Ray Diffraction 1.5397 1.5814 -- 130 2549 0.2794 0.3004 -- 91.0
X Ray Diffraction 1.5814 1.6279 -- 125 2628 0.2391 0.2711 -- 93.0
X Ray Diffraction 1.6279 1.6804 -- 127 2619 0.2187 0.2968 -- 93.0
X Ray Diffraction 1.6804 1.7405 -- 152 2654 0.2135 0.2565 -- 94.0
X Ray Diffraction 1.7405 1.8102 -- 124 2703 0.1965 0.1938 -- 96.0
X Ray Diffraction 1.8102 1.8925 -- 145 2705 0.1775 0.2522 -- 96.0
X Ray Diffraction 1.8925 1.9923 -- 157 2729 0.1661 0.2269 -- 97.0
X Ray Diffraction 1.9923 2.1171 -- 143 2809 0.1582 0.1758 -- 99.0
X Ray Diffraction 2.1171 2.2805 -- 152 2799 0.1666 0.2083 -- 99.0
X Ray Diffraction 2.2805 2.5099 -- 136 2848 0.167 0.2414 -- 99.0
X Ray Diffraction 2.5099 2.8729 -- 158 2829 0.1843 0.2139 -- 99.0
X Ray Diffraction 2.8729 3.6187 -- 167 2878 0.1728 0.1804 -- 100.0
X Ray Diffraction 3.6187 31.1712 -- 167 2956 0.1711 0.1828 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.08
f_bond_d 0.007
f_dihedral_angle_d 14.438
f_plane_restr 0.005
f_angle_d 1.129
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2229
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 266

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.8_1069)
HKL-2000 data reduction
SCALEPACK data scaling
Coot model building