X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Details 5mM TRIS(HCl), 23mM CaAcetate, 16% MPD, .6mM DNA against 28% MPD at RT, pH 7.50, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 32.96 α = 90
b = 32.96 β = 90
c = 88.56 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 103
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 BENT CONICAL SI-MIRROR (RH COATING) 2002-01-08
Diffraction Radiation
Monochromator Protocol
BENT GE(111) MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C

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
1.85 17.5 96.3 0.056 -- -- -- 2528 2528 -- 0.0 8.8
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)
1.85 1.92 72.2 0.245 -- 4.98 -- --

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 1.9 17.49 0.0 0.0 2528 2413 228 93.9 0.253 0.232 0.232 0.258 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 1.9 2.02 -- 34 287 0.308 0.4 0.069 80.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.0
Anisotropic B[1][1] 3.22
Anisotropic B[1][2] 3.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.45
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.6
c_bond_d 0.067
c_improper_angle_d 5.46
c_angle_deg 6.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 203
Heterogen Atoms 3
Solvent Atoms 40

Software

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