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_scangle_it 24.14
c_scbond_it 19.26
c_mcangle_it 17.4
c_mcbond_it 12.23
c_improper_angle_d 1.05
c_dihedral_angle_d 22.2
c_angle_deg 1.5
c_bond_d 0.009
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 8944
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 209

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building