X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details Protein solution (1.5mcl): 13mg/ml Asbeta-Gly, 0.025M NaCl, 0.025M Hepes (pH 7.5). Reservoir solution (1.5mcl): 1.0M succinic acid (pH 7.0), 0.1M Hepes (pH 7.0), 1% w/v polyethylene glycol monomethyl ether 2000. The crystal was soaked in a cryoprotection solution containing 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.12 α = 90
b = 84.12 β = 90
c = 166.27 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2010-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.9815 KURCHATOV SNC K4.4

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
1.37 19.83 98.8 0.063 -- -- -- -- 124046 -- -- 20.1
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)
1.37 1.45 96.5 0.81 -- 2.1 -- 18722

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 1.37 19.827 -- -- -- 117803 6243 98.83 -- 0.13213 0.13049 0.16333 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 1.37 1.406 -- 432 8083 0.24 0.282 -- 93.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.182
Anisotropic B[1][1] -0.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.55
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.704
r_sphericity_free 7.943
r_rigid_bond_restr 1.387
r_scangle_it 3.974
r_scbond_it 2.945
r_mcangle_it 2.075
r_mcbond_other 0.722
r_bond_refined_d 0.015
r_bond_other_d 0.001
r_angle_refined_deg 1.559
r_angle_other_deg 0.927
r_dihedral_angle_1_deg 6.226
r_dihedral_angle_2_deg 32.875
r_dihedral_angle_3_deg 12.343
r_dihedral_angle_4_deg 15.576
r_chiral_restr 0.114
r_gen_planes_refined 0.009
r_gen_planes_other 0.001
r_mcbond_it 1.478
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.134
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3909
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 543

Software

Computing
Computing Package Purpose
Automar Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
BALBES Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
BALBES model building
Automar data collection