X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details ammonium sulfate, PEG 4000, acetate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.98 α = 90
b = 57.48 β = 119.39
c = 114.63 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 133
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9236 SPRING-8 BL38B1

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
1.4 29.85 85.4 0.036 -- -- 5.8 172073 146871 -- -3.0 24.5
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)
1.4 1.42 49.1 0.258 -- 2.0 -- --

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 1.42 29.85 0.0 0.0 164652 136219 6898 82.7 -- -- 0.229 0.255 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 1.42 1.48 12380 617 11763 0.342 0.362 0.014 60.4
X Ray Diffraction 1.48 1.56 14018 745 13273 0.296 0.323 0.011 68.3
X Ray Diffraction 1.56 1.66 15160 761 14399 0.275 0.29 0.01 73.9
X Ray Diffraction 1.66 1.79 16485 838 15647 0.26 0.283 0.009 80.1
X Ray Diffraction 1.79 1.97 17971 911 17060 0.239 0.254 0.008 87.5
X Ray Diffraction 1.97 2.25 19891 1009 18882 0.244 0.271 0.008 96.6
X Ray Diffraction 2.25 2.84 20412 1041 19371 0.234 0.262 0.007 98.8
X Ray Diffraction 2.84 29.85 19902 976 18926 0.205 0.232 0.007 95.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 30.32
Anisotropic B[1][1] 0.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.41
Anisotropic B[2][2] -6.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.34
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 5.83
c_scbond_it 4.18
c_mcangle_it 3.26
c_mcbond_it 2.27
c_improper_angle_d 0.76
c_dihedral_angle_d 24.0
c_angle_deg 1.3
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6148
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 756

Software

Computing
Computing Package Purpose
ADSC Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
SCALEPACK data reduction
ADSC version: quantum software data collection