X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.3
Temperature 285.0
Details initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 mM dipotassium hydrogenphosphate], 3 ul 1 mM adenylyl imidodiphosphate (AMPPNP), 3 ul 2 mM magnesium chloride, 2 ul 10 % (w/v) polyethylene glycol 400 dodecylether (Thesit), pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 175.99 α = 90
b = 175.99 β = 90
c = 93.67 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-01-26
Diffraction Radiation
Monochromator Protocol
silicon 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8428 EMBL/DESY, Hamburg BW7B

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
3.1 59.3 98.4 -- 0.096 -- 8.8 -- 29935 0.0 0.0 92.2
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)
3.1 3.2 90.4 -- 42.0 2.6 6.0 --

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 3.1 59.3 -- 0.0 -- 23733 935 78.7 -- -- 0.267 0.338 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 3.1 3.24 2325 81 2244 0.458 0.458 0.051 62.2
X Ray Diffraction 3.24 3.41 2604 95 2509 0.347 0.352 0.036 69.7
X Ray Diffraction 3.41 3.63 2752 108 2644 0.32 0.328 0.032 73.0
X Ray Diffraction 3.63 3.91 3051 125 2926 0.289 0.291 0.026 81.0
X Ray Diffraction 3.91 4.3 2702 96 2606 0.223 0.218 0.022 72.0
X Ray Diffraction 4.3 4.92 3152 134 3018 0.215 0.202 0.017 83.6
X Ray Diffraction 4.92 6.2 3378 142 3236 0.262 0.237 0.02 89.4
X Ray Diffraction 6.2 59.11 3769 154 3615 0.242 0.254 0.02 97.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 90.96
Anisotropic B[1][1] -32.76
Anisotropic B[1][2] 26.71
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -32.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 65.51
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.5
c_scbond_it 19.26
c_mcangle_it 17.4
c_improper_angle_d 1.05
c_mcbond_it 12.23
c_scangle_it 24.14
c_bond_d 0.009
c_dihedral_angle_d 22.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.46
Luzzati Sigma A (Observed) 0.88
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.6
Luzzati Sigma A (R-Free Set) 1.05
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8947
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 209

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling