X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 10 mM Magnesium acetate, 50 mM Sodium cacodylate, 1.3 M Lithium sulfate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.97 α = 90
b = 74.97 β = 90
c = 74.97 γ = 90
Symmetry
Space Group P 43 3 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2003-05-05
CCD ADSC QUANTUM 4 -- 2005-03-05
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal SINGLE WAVELENGTH
Single Silicon (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM16 1.739 ESRF BM16
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9763 ESRF ID14-4

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
2.5 18.18 99.6 0.074 -- -- 15.9 2766 2766 -- -3.0 --
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)
2.5 2.6 100.0 0.798 -- 4.08 13.7 --

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
SAD 2.5 18.18 -- -- -- 2629 127 100.0 -- 0.24546 0.24482 0.25918 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 2.5 2.564 -- 9 170 0.508 0.427 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 55.027
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.53
r_scbond_it 2.131
r_gen_planes_refined 0.008
r_chiral_restr 0.11
r_angle_refined_deg 2.083
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 240
Heterogen Atoms 267
Solvent Atoms 5

Software

Computing
Computing Package Purpose
MXCuBe Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXC/D/E Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0066 refinement
SHELXC/D/E model building
MXCuBe data collection