X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 12 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 20% (V/V) ISOPROPANOL, 2% (W/V) PEG 1500, IN 100 MM CITRIC ACID BROUGHT TO PH 5.5 WITH NAOH. CRYSTALS GROW AT 4 DEG. C AND TAKE UP TO 8 WEEKS TO REACH FULL SIZE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.57 α = 90
b = 41.76 β = 90
c = 54.53 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM MIRRORS 2000-02-15
Diffraction Radiation
Monochromator Protocol
DIAMOND C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

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
1.35 40 97.9 0.047 -- -- 3.8 -- 38263 -- -3.0 12.7
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)
1.35 1.4 83.4 0.142 -- 5.2 2.7 --

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
MAD 1.35 40.0 -- 0.0 -- 38263 1921 97.9 -- -- 0.184 0.213 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.7
RMS Deviations
Key Refinement Restraint Deviation
p_transverse_tor 19.5
p_staggered_tor 13.1
p_planar_tor 5.8
p_multtor_nbd 0.257
p_bond_d 0.011
p_angle_d 0.029
p_planar_d 0.036
p_mcbond_it 2.299
p_mcangle_it 3.073
p_scbond_it 3.371
p_scangle_it 4.333
p_plane_restr 0.0323
p_chiral_restr 0.106
p_singtor_nbd 0.173
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1423
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 149

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
SOLVE model building