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 CONCENTRATION 5 MG/ML FUCOSE WAS INTRODUCED BY SHORT SOAKING OF A NATIVE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 179.08 α = 90
b = 179.08 β = 90
c = 174.69 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 -- 2001-09-16
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
2.8 57.7 98.1 0.056 -- -- 3.9 -- 24598 -- -- 100.81
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)
2.8 2.87 98.1 0.442 -- 1.6 3.9 --

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 2.8 19.76 -- -- -- 24054 1848 97.5 -- 0.203 0.201 0.23 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 2.8 2.87 -- 128 1762 0.31 0.354 -- --
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.32
Anisotropic B[1][2] -1.16
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.49
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.193
r_gen_planes_refined 0.005
r_nbd_other 0.212
r_scangle_it 0.989
r_bond_other_d 0.005
r_xyhbond_nbd_refined 0.136
r_angle_refined_deg 0.987
r_chiral_restr 0.058
r_scbond_it 0.567
r_angle_other_deg 0.757
r_gen_planes_other 0.007
r_bond_refined_d 0.007
r_symmetry_vdw_other 0.2
r_mcangle_it 0.573
r_dihedral_angle_1_deg 4.968
r_nbtor_other 0.082
r_mcbond_it 0.304
r_nbd_refined 0.17
r_symmetry_vdw_refined 0.091
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7004
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 0

Software

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