X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 4.5
Temperature 297.0
Details PEG 4000, NH4OAc, pH 4.5, microbatch, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.1 α = 90
b = 154.44 β = 90
c = 164.01 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 Nonius Kappa CCD mirrors 2004-08-29
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE Cu FINE FOCUS 1.54 -- --

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
2.3 50 99.3 0.082 -- -- -- -- 63667 0.0 33.9 28.0
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)
2.3 2.38 96.0 0.468 -- 2.34 -- 6034

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 2.3 44.62 1.0 0.0 64107 63588 3186 98.9 -- -- 0.2217 0.2596 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 2.3 2.41 7527 405 830 0.286 0.306 0.015 95.3
X Ray Diffraction 2.41 2.53 7827 348 1174 0.277 0.325 0.017 98.6
X Ray Diffraction 2.53 2.69 7883 416 1177 0.259 0.295 0.014 99.5
X Ray Diffraction 2.69 2.9 7934 388 1130 0.238 0.278 0.014 99.8
X Ray Diffraction 2.9 3.19 7947 411 1193 0.219 0.279 0.014 99.8
X Ray Diffraction 3.19 3.65 8007 380 1172 0.199 0.242 0.012 99.8
X Ray Diffraction 3.65 4.6 8080 424 1194 0.185 0.21 0.01 99.9
X Ray Diffraction 4.6 44.62 8383 414 1211 0.212 0.25 0.012 99.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 43.0398
Anisotropic B[1][1] 4.961
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.722
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.239
RMS Deviations
Key Refinement Restraint Deviation
c_torsion_impr_deg 0.77
c_torsion_deg 23.0
c_scangle_it 2.74
c_mcangle_it 2.49
c_angle_deg 1.4
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9044
Nucleic Acid Atoms 0
Heterogen Atoms 170
Solvent Atoms 313

Software

Computing
Computing Package Purpose
supergui Data Collection
HKL2000 Data Reduction (intensity integration)
HKL2000 Data Reduction (data scaling)
CNS Structure Solution
CNS 1.2 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
CNS refinement
CNS molecular replacement
SCALEPACK data scaling
DENZO reflection data processing