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 = 76.22 α = 90
b = 41.75 β = 90
c = 54.51 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 CCD -- 2000-08-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 -- SRS PX9.6

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 40 98.1 0.059 -- -- 3.2 -- 12166 -- -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)
2.0 2.07 86.9 0.163 -- 4.4 -- --

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 2.0 54.23 -- -- -- 11556 610 99.0 -- -- 0.171 0.226 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 2.0 2.05 -- 31 786 0.151 0.281 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.73
Anisotropic B[1][1] -0.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.253
r_chiral_restr 0.132
r_scangle_it 4.876
r_xyhbond_nbd_refined 0.188
r_dihedral_angle_1_deg 7.514
r_scbond_it 3.014
r_mcangle_it 2.179
r_gen_planes_refined 0.008
r_angle_refined_deg 1.851
r_bond_refined_d 0.02
r_nbd_refined 0.222
r_symmetry_hbond_refined 0.207
r_mcbond_it 1.251
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1431
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 164

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling