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 -- 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_scangle_it 3.876
r_scbond_it 2.69
r_mcangle_it 2.046
r_mcbond_it 1.358
r_nbd_refined 0.213
r_gen_planes_other 0.009
r_gen_planes_refined 0.012
r_chiral_restr 0.123
r_dihedral_angle_1_deg 6.433
r_angle_other_deg 2.13
r_angle_refined_deg 1.766
r_bond_other_d 0.001
r_bond_refined_d 0.016
r_nbd_other 0.273
r_nbtor_other 0.081
r_xyhbond_nbd_refined 0.162
r_symmetry_vdw_refined 0.163
r_symmetry_vdw_other 0.274
r_symmetry_hbond_refined 0.127
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

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