X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details MPD, Spermine, KCl, Sodium Cacodylate, pH 6.0. VAPOR DIFFUSION, HANGING DROP at 295 K, temperature 295.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 26.14 α = 90
b = 43.96 β = 90
c = 45.8 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-03-31
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 0.93217 APS 5ID-B

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
1.4 20 99.7 0.049 -- -- 8.6 10950 10950 0.0 -3.0 --
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)
1.4 1.45 96.7 0.26 -- 6.8 6.0 1038

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 1.4 17.0 0.0 0.0 10660 10660 1036 97.5 -- -- 0.167 0.174 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 1.4 1.45 -- 79 -- 0.2589 0.2828 -- 0.941
X Ray Diffraction 1.45 1.51 -- 106 -- 0.2201 0.2369 -- 0.954
X Ray Diffraction 1.51 1.58 -- 105 -- 0.2036 0.2271 -- 0.965
X Ray Diffraction 1.58 1.66 -- 106 -- 0.1653 0.1923 -- 0.975
X Ray Diffraction 1.66 1.76 -- 107 -- 0.1627 0.2111 -- 0.984
X Ray Diffraction 1.76 1.9 -- 90 -- 0.1595 0.1683 -- 0.983
X Ray Diffraction 1.9 2.09 -- 111 -- 0.1728 0.2062 -- 0.991
X Ray Diffraction 2.09 2.39 -- 108 -- 0.1709 0.1807 -- 0.995
X Ray Diffraction 2.39 3.01 -- 126 -- 0.173 0.1827 -- 0.998
X Ray Diffraction 3.01 17.0 -- 98 -- 0.1497 0.1307 -- 0.998
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.5
Anisotropic B[1][1] -1.542
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.174
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.632
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.009
c_improper_angle_d 1.62
c_angle_deg 1.51
c_dihedral_angle_d 27.46
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 416
Heterogen Atoms 0
Solvent Atoms 128

Software

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