X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details 18 % PEG600, 5 % JEFFAMINE, M-600 100 MM TRIS-HCL PH 8.0, PROTEIN CONC. 5 MG/ML

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 172.46 α = 90
b = 172.46 β = 90
c = 167.41 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2001-03-03
Diffraction Radiation
Monochromator Protocol
-- 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
2.4 37.3 99.1 0.069 -- -- 5.7 -- 36833 -- -- --
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)
2.4 2.46 99.1 0.416 -- 1.8 5.4 --

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
MAD 2.4 37.27 -- -- -- 34433 2642 99.1 -- 0.188 0.185 0.228 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 2.4 2.46 -- 197 2487 0.222 0.282 -- --
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.23
Anisotropic B[1][2] 0.62
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.85
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_symmetry_hbond_refined 0.134
r_bond_refined_d 0.008
r_symmetry_vdw_refined 0.092
r_scangle_it 1.621
r_symmetry_vdw_other 0.219
r_mcbond_it 0.361
r_chiral_restr 0.069
r_mcangle_it 0.689
r_xyhbond_nbd_refined 0.153
r_nbtor_other 0.083
r_scbond_it 0.966
r_nbd_other 0.213
r_bond_other_d 0.002
r_angle_other_deg 0.782
r_angle_refined_deg 1.103
r_gen_planes_refined 0.004
r_nbd_refined 0.18
r_dihedral_angle_1_deg 5.943
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7037
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 162

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALA data scaling
SOLVE phasing