X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details Protein solution (1.5mcl): 15mg/ml Asbeta-Gly, 0.025M NaCl, 0.05M Tris (pH 8.0). Reservoir solution (1.5mcl): 0.04M cellobiose, 0.16M magnesium acetate, 0.08M sodium cacodylate (pH 6.5), 16% w/v polyethylene glycol 8000, 20% v/v glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.18 α = 90
b = 84.18 β = 90
c = 166.22 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 0.9779 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
1.46 19.84 98.0 0.063 -- -- -- 102050 102050 -- -- 20.3
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)
1.46 1.55 91.1 0.519 -- 4.5 -- 15340

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 1.46 19.841 -- -- -- 96870 5109 97.96 -- 0.14394 0.14314 0.15886 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 1.46 1.498 -- 322 6135 0.23 0.25 -- 85.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.262
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.51
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.081
r_scbond_it 1.975
r_mcangle_it 1.337
r_mcbond_other 0.228
r_bond_refined_d 0.015
r_bond_other_d 0.001
r_angle_refined_deg 1.531
r_angle_other_deg 0.882
r_dihedral_angle_1_deg 6.175
r_dihedral_angle_2_deg 33.266
r_dihedral_angle_3_deg 11.759
r_dihedral_angle_4_deg 16.422
r_chiral_restr 0.099
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_mcbond_it 0.774
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.134
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3906
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 516

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