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 Crystals appeared after one week; Crystallization conditions: 40mg/ml yeast 20S proteasome 0.1M MES; 28mM MgAc2, 12% MPD 6h crystal soak with 10mM SalA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.17 α = 90
b = 301.16 β = 112.82
c = 144.14 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2004-12-16
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6

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
2.8 15 100.0 -- -- -- -- 255532 255532 2.0 2.0 50.7
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)
2.82 2.87 99.8 0.467 -- -- -- 271888

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
FOURIER SYNTHESIS 2.8 15.0 -- 0.0 258110 242755 12668 99.1 0.23 0.229 0.229 0.254 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 2.8 2.97 -- 2116 40666 0.352 0.381 0.008 99.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 51.2
Anisotropic B[1][1] 5.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -12.81
Anisotropic B[2][2] -15.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.21
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_angle_deg 1.3
c_dihedral_angle_d 23.2
c_improper_angle_d 0.77
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.54
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.59
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 49548
Nucleic Acid Atoms 0
Heterogen Atoms 120
Solvent Atoms 1017

Software

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
CNS phasing