X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details PROTEIN SOLUTION: 10 MM TRIS (PH 8.0), 1 MM DTT, 1 MM EDTA, 28.8 MG/ML PROTEIN COMPLEX. PRECIPITATE SOLUTION: 15 %[W/V] PEG-8000, 0.9 M AMMONIUM NITRATE, 0.1 M HEPES/HCL (PH 8.5), 10 MM DTT, 5% [V/V] MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74 α = 90
b = 91.9 β = 105.9
c = 131 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 X-RAY RESEARCH BENT MIRROR --
Diffraction Radiation
Monochromator Protocol
TRIANGULAR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 -- EMBL/DESY, Hamburg X11

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
2.37 30 96.7 0.048 -- -- 2.9 -- 65356 -- -- 46.2
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)
2.37 2.45 78.8 0.168 -- 4.5 2.5 --

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 2.4 30.0 -- 0.0 -- 65356 3327 97.8 -- 0.226 0.226 0.29 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 2.4 2.55 -- 529 9566 0.311 0.406 0.018 91.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 58.4
Anisotropic B[1][1] 22.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.36
Anisotropic B[2][2] -9.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -13.33
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.8
c_scbond_it 13.34
c_mcangle_it 9.73
c_mcbond_it 9.63
c_angle_deg 1.5
c_bond_d 0.008
c_scangle_it 13.92
c_improper_angle_d 0.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.47
Luzzati Sigma A (R-Free Set) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10643
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 459

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing