X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.4
Details DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO, 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 4% GLYCEROL, 1 MM DGTP.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.92 α = 90
b = 103.83 β = 90
c = 52.49 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MIRRORS 2008-07-25
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID -- APS 22-ID

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
3 42.11 99.6 0.08 -- -- 6.6 -- 11751 -- 0.0 57.3
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)
3.0 3.19 100.0 0.77 -- 4.7 7.3 --

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 3.0 29.25 -- 0.0 -- 10584 560 98.5 -- 0.226 0.226 0.282 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 3.0 3.19 -- 88 1607 0.325 0.4 0.043 97.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 77.4
Anisotropic B[1][1] 5.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.09
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.6
c_mcbond_it 1.5
c_mcangle_it 2.61
c_dihedral_angle_d 22.2
c_scangle_it 3.5
c_improper_angle_d 1.77
c_bond_d 0.009
c_scbond_it 2.25
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.36
Luzzati Resolution Cutoff (Low) 30.0
Luzzati ESD (R-Free Set) 0.54
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2754
Nucleic Acid Atoms 618
Heterogen Atoms 34
Solvent Atoms 43

Software

Software
Software Name Purpose
CNS refinement version: 1.2
HKL-2000 data reduction
SCALEPACK data scaling
MOLREP phasing