X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.2
Details PROTEIN WAS USED AT A CONCENTRATION OF 10MG/ML. IT WAS INCUBATED WITH 5MM CELLOBIO-DERIVED ISOFAGOMINE FOR AN HOUR PRIOR CRYSTALLISATION. THE VAPOR DIFFUSION METHOD WAS USED. 1.3 M AMMONIUM SULPHATE WERE USED AS PRECIPITANT. 20 % GLYCEROL WAS ADDED FOR CRYOPROTECTION, pH 5.20

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.02 α = 90
b = 69.68 β = 90
c = 76.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2002-01-15
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
1.08 15 99.7 0.07 -- -- 4.3 -- 126591 -- -- --
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)
1.08 1.1 99.9 0.377 -- 3.8 4.1 --

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 1.08 14.96 -- -- -- 119168 6322 99.1 -- 0.115 0.115 0.127 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 1.08 1.11 -- 476 8574 0.159 0.17 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.47
Anisotropic B[1][1] 1.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.58
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.213
r_angle_other_deg 2.13
r_symmetry_hbond_refined 0.127
r_symmetry_vdw_other 0.274
r_mcangle_it 2.046
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.162
r_nbd_other 0.273
r_chiral_restr 0.123
r_bond_other_d 0.001
r_angle_refined_deg 1.766
r_symmetry_vdw_refined 0.163
r_mcbond_it 1.358
r_scbond_it 2.69
r_nbtor_other 0.081
r_gen_planes_other 0.009
r_dihedral_angle_1_deg 6.433
r_scangle_it 3.876
r_gen_planes_refined 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2377
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 445

Software

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