5MQV

Crystal structure of human Casein Kinase I delta in complex with 4-(2,5-Dimethoxyphenyl)-N-(4-(5-(4-fluorphenyl)-2-(methylthio)-1H-imidazol-4-yl)-pyridin-2-yl)-1-methyl-1H-pyrrole-2-carboxamide


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 0.1 M Hepes pH 7.0, 0.7 M NaH2PO4, 0.7 M KH2PO4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 197.93 α = 90
b = 127.28 β = 113.63
c = 154.78 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
PIXEL DECTRIS PILATUS 2M-F -- 2016-08-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA

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
2.15 49.29 99.0 0.06 -- -- 4.5 -- 187597 -- -- --
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)
2.154 2.231 94.0 0.45 -- 2.49 4.3 17796

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 2.154 49.291 -- 1.36 -- 363083 3864 97.06 -- 0.1733 0.1731 0.1917 --
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 2.1544 2.1807 -- 117 10739 0.2589 0.2657 0.0 81.0
X Ray Diffraction 2.1807 2.2083 -- 143 13011 0.2379 0.2388 0.0 99.0
X Ray Diffraction 2.2083 2.2374 -- 137 12900 0.2287 0.2467 0.0 98.0
X Ray Diffraction 2.2374 2.268 -- 141 13126 0.2189 0.2378 0.0 99.0
X Ray Diffraction 2.268 2.3004 -- 142 13163 0.2143 0.2526 0.0 100.0
X Ray Diffraction 2.3004 2.3348 -- 141 13161 0.2153 0.2595 0.0 100.0
X Ray Diffraction 2.3348 2.3713 -- 140 13131 0.2067 0.2326 0.0 100.0
X Ray Diffraction 2.3713 2.4101 -- 142 13221 0.2024 0.2585 0.0 100.0
X Ray Diffraction 2.4101 2.4517 -- 144 13222 0.1975 0.202 0.0 100.0
X Ray Diffraction 2.4517 2.4963 -- 142 13186 0.1852 0.1674 0.0 99.0
X Ray Diffraction 2.4963 2.5443 -- 140 13024 0.1808 0.1976 0.0 99.0
X Ray Diffraction 2.5443 2.5962 -- 143 13181 0.179 0.2495 0.0 100.0
X Ray Diffraction 2.5962 2.6527 -- 141 13136 0.179 0.1992 0.0 99.0
X Ray Diffraction 2.6527 2.7144 -- 143 13141 0.1827 0.2132 0.0 99.0
X Ray Diffraction 2.7144 2.7822 -- 142 13114 0.1778 0.2318 0.0 99.0
X Ray Diffraction 2.7822 2.8575 -- 141 13064 0.1829 0.2026 0.0 99.0
X Ray Diffraction 2.8575 2.9415 -- 133 12967 0.1803 0.2081 0.0 98.0
X Ray Diffraction 2.9415 3.0365 -- 137 12647 0.1872 0.2221 0.0 96.0
X Ray Diffraction 3.0365 3.145 -- 135 12567 0.1913 0.2025 0.0 96.0
X Ray Diffraction 3.145 3.2709 -- 138 12686 0.1777 0.2055 0.0 95.0
X Ray Diffraction 3.2709 3.4197 -- 133 12646 0.1774 0.1954 0.0 96.0
X Ray Diffraction 3.4197 3.5999 -- 139 12702 0.1697 0.1809 0.0 96.0
X Ray Diffraction 3.5999 3.8254 -- 138 12679 0.1656 0.1563 0.0 96.0
X Ray Diffraction 3.8254 4.1206 -- 136 12561 0.1464 0.1429 0.0 95.0
X Ray Diffraction 4.1206 4.535 -- 130 12522 0.1306 0.1627 0.0 95.0
X Ray Diffraction 4.535 5.1906 -- 130 12464 0.1307 0.1493 0.0 95.0
X Ray Diffraction 5.1906 6.5373 -- 140 12392 0.1794 0.1755 0.0 94.0
X Ray Diffraction 6.5373 49.3035 -- 136 12866 0.179 0.2037 0.0 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.0082
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.042
f_dihedral_angle_d 13.635
f_plane_restr 0.003
f_bond_d 0.003
f_angle_d 0.646
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13805
Nucleic Acid Atoms 0
Heterogen Atoms 495
Solvent Atoms 697

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.22
XDS data scaling version: May 1, 2016
PHASER phasing version: 1.10.1_2155
XDS data reduction