X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 294.0
Details Ammonium Sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.41 α = 90
b = 76.99 β = 106.15
c = 43.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Quartz crystal 2000-07-15
Diffraction Radiation
Monochromator Protocol
Quartz crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 0.9500 PHOTON FACTORY BL-18B
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 0.9793 PHOTON FACTORY BL-18B
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 0.9795 PHOTON FACTORY BL-18B

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
1.9 14.97 98.5 0.046 -- -- 4.0 20164 83143 0.0 4.0 10.1
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)
1.9 1.99 98.5 0.155 -- -- 4.0 --

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
MAD 1.9 14.97 4.0 2.0 20453 20149 1987 98.5 0.19 0.19 0.188 0.222 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 1.9 1.99 2466 239 2227 0.221 0.219 0.014 97.0
X Ray Diffraction 1.99 2.09 2485 238 2247 0.184 0.183 0.012 97.8
X Ray Diffraction 2.09 2.22 2498 266 2232 0.183 0.183 0.011 97.8
X Ray Diffraction 2.22 2.39 2524 259 2265 0.179 0.18 0.011 98.6
X Ray Diffraction 2.39 2.63 2507 235 2272 0.188 0.188 0.012 98.6
X Ray Diffraction 2.63 3.01 2536 244 2292 0.204 0.204 0.013 98.6
X Ray Diffraction 3.01 3.78 2542 237 2305 0.185 0.186 0.012 99.4
X Ray Diffraction 3.78 14.97 2591 269 2322 0.178 0.177 0.011 99.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 14.51
Anisotropic B[1][1] -0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.41
Anisotropic B[2][2] 0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.32
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 0.9
x_torsion_deg 22.4
x_angle_deg 1.2
x_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2256
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 269

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHARP Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SHARP model building