X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details 50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME, RT, CRYSTALLIZED FROM FULL LENGTH APOE4 CONSTRUCT (299 RESIDUES). PROTEOLYTIC CLEAVAGE IN CRYSTALLIZATION DROP TO 22K FRAGMENT. NEW, THIRD ORTHOGONAL CRYSTAL FORM OF APOE (ORTHO-3)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.51 α = 90
b = 53.09 β = 90
c = 73.37 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 125
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD MIRRORS 1999-04-15
Diffraction Radiation
Monochromator Protocol
SI SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 -- ALS 5.0.2

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
1.7 20.9 99.97 -- 0.035 -- 7.7 -- 20168 -- -- --

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 1.7 20.9 -- -- -- 19116 1045 100.0 -- 0.219 0.218 0.247 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 1.7 1.72 -- 38 696 0.304 0.429 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.25
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.592
r_angle_refined_deg 1.794
r_mcbond_it 1.237
r_bond_refined_d 0.016
r_nbd_refined 0.232
r_xyhbond_nbd_refined 0.222
r_scangle_it 4.111
r_symmetry_vdw_refined 0.257
r_scbond_it 2.507
r_mcangle_it 2.354
r_dihedral_angle_1_deg 4.161
r_symmetry_hbond_refined 0.232
r_gen_planes_refined 0.008
r_chiral_restr 0.117
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1179
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 223

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
MOSFLM data reduction
SCALA data scaling
EPMR phasing