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 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_scangle_it 4.111
r_scbond_it 2.507
r_mcangle_it 2.354
r_mcbond_it 1.237
r_nbd_refined 0.232
r_gen_planes_refined 0.008
r_chiral_restr 0.117
r_dihedral_angle_3_deg 16.592
r_dihedral_angle_1_deg 4.161
r_angle_refined_deg 1.794
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.222
r_symmetry_vdw_refined 0.257
r_symmetry_hbond_refined 0.232
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
EPMR Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
EPMR model building