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 -- 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_scangle_it 1.621
r_scbond_it 0.966
r_mcangle_it 0.689
r_mcbond_it 0.361
r_nbd_refined 0.18
r_gen_planes_other 0.002
r_gen_planes_refined 0.004
r_chiral_restr 0.069
r_dihedral_angle_1_deg 5.943
r_angle_other_deg 0.782
r_angle_refined_deg 1.103
r_bond_other_d 0.002
r_bond_refined_d 0.008
r_nbd_other 0.213
r_nbtor_other 0.083
r_xyhbond_nbd_refined 0.153
r_symmetry_vdw_refined 0.092
r_symmetry_vdw_other 0.219
r_symmetry_hbond_refined 0.134
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SOLVE model building