X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 2-[N-morpholino]ethanesulfonic acid, PEGMME 5000, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.94 α = 90
b = 49.94 β = 90
c = 170.36 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 133
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
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
1.9 28.15 97.0 0.046 -- -- 20.96 17352 17352 0.0 0.0 26.6
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 1.97 87.2 0.246 -- 4.94 -- --

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 1.9 28.15 -- 0.0 17893 16976 1695 94.9 -- -- 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 1.9 2.02 2437 225 2212 0.324 0.313 0.022 83.7
X Ray Diffraction 2.02 2.17 2832 254 2578 0.283 0.34 0.018 96.9
X Ray Diffraction 2.17 2.39 2872 295 2577 0.251 0.29 0.015 98.2
X Ray Diffraction 2.39 2.74 2906 302 2604 0.24 0.286 0.014 98.4
X Ray Diffraction 2.74 3.45 2956 318 2638 0.244 0.283 0.014 98.9
X Ray Diffraction 3.45 28.15 2973 301 2672 0.222 0.263 0.013 92.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 46.8
Anisotropic B[1][1] 8.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.46
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.1
x_dihedral_angle_d 21.3
x_improper_angle_d 0.79
x_bond_d 0.006
x_scangle_it 3.06
x_mcangle_it 2.75
x_mcbond_it 1.64
x_scbond_it 2.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1416
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 147

Software

Software
Software Name Purpose
CNS refinement version: 1.0
ADSC data collection version: (QUANTUM)
SCALEPACK data scaling
CNS phasing