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_scangle_it 3.06
x_scbond_it 2.0
x_mcangle_it 2.75
x_mcbond_it 1.64
x_improper_angle_d 0.79
x_dihedral_angle_d 21.3
x_angle_deg 1.1
x_bond_d 0.006
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

Computing
Computing Package Purpose
ADSC (QUANTUM) Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement