X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.25
Temperature 293.0
Details PEG 6K, lithium chloride, cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.35 α = 90
b = 94.35 β = 90
c = 186.55 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC Yale mirrors 1997-07-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R 1.5418 -- --

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
2.8 34.92 94.7 0.075 -- -- 3.9 21507 20430 0.0 0.0 68.8
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)
2.8 2.9 89.0 0.332 -- 2.5 -- --

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
Difference fourier 2.8 34.92 0.0 0.0 21507 20416 2008 94.9 0.238 0.238 0.227 0.281 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 2.8 2.93 2354 231 2123 0.325 0.353 0.023 89.2
X Ray Diffraction 2.93 3.08 2404 243 2161 0.306 0.354 0.023 91.4
X Ray Diffraction 3.08 3.27 2470 271 2199 0.276 0.321 0.019 93.1
X Ray Diffraction 3.27 3.53 2512 240 2272 0.251 0.304 0.02 95.4
X Ray Diffraction 3.53 3.88 2590 234 2356 0.22 0.278 0.018 97.1
X Ray Diffraction 3.88 4.44 2611 253 2358 0.203 0.27 0.017 97.1
X Ray Diffraction 4.44 5.59 2673 257 2416 0.189 0.242 0.015 98.1
X Ray Diffraction 5.59 34.92 2802 279 2523 0.207 0.261 0.016 97.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 49.83
Anisotropic B[1][1] 3.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.75
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.36
x_scbond_it 1.49
x_mcangle_it 1.82
x_mcbond_it 1.04
x_torsion_impr_deg 0.98
x_torsion_deg 23.7
x_angle_deg 1.4
x_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Sigma A (Observed) 0.51
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.57
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4063
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 32

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.1 refinement