X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 290.0
Details 25% PEG8000, 5mM MgCl2, 400 mM NaCl, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.92 α = 85.84
b = 52.02 β = 76.61
c = 78.88 γ = 74.48
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR MARRESEARCH segmented mirror 1997-12-15
Diffraction Radiation
Monochromator Protocol
single crystal germanium triangular monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9054 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
2.35 19.6 75.0 0.083 -- -- 2.8 25370 25370 0.0 0.0 49.8
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)
2.35 2.43 0.49 0.393 -- 2.5 2.1 --

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 19.6 0.0 0.0 19630 19630 1940 75.0 0.2357 0.2357 0.253 0.299 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 2.49 -- 165 2640 0.3895 0.4156 0.026 63.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.0
Anisotropic B[1][1] 30.65
Anisotropic B[1][2] 7.4
Anisotropic B[1][3] -2.34
Anisotropic B[2][2] -17.89
Anisotropic B[2][3] -4.41
Anisotropic B[3][3] -12.77
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 20.3
c_bond_d 0.007
c_mcbond_it 2.92
c_scbond_it 5.33
c_scangle_it 7.71
c_angle_deg 1.3
c_mcangle_it 4.63
c_improper_angle_d 1.03
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.58
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.62
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2363
Nucleic Acid Atoms 1628
Heterogen Atoms 8
Solvent Atoms 279

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.9
MAR345 data collection
SCALEPACK data scaling