X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.6
Details THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M CITRATE, PH 5.4 - 5.8; 20 MM NACL, 2 MM EDTA., pH 5.60, VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.4 α = 90
b = 113.4 β = 90
c = 88.2 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV YALE MIRRORS 1998-03-15
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.2 50 94.8 0.035 0.035 -- 3.58 -- 31357 -- 2.0 --
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)
2.2 2.24 75.8 0.093 0.093 8.0 3.58 --

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
MIR 2.2 100.0 -- -- -- 31357 1275 94.8 -- 0.216 0.216 0.265 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 2.2 2.3 -- 124 3048 0.285 0.311 -- 73.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.0
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 27.5
x_bond_d 0.008
x_angle_deg 1.3
x_improper_angle_d 1.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2490
Nucleic Acid Atoms 854
Heterogen Atoms 4
Solvent Atoms 226

Software

Software
Software Name Purpose
PHASES phasing
X-PLOR refinement version: 3.843
DENZO data reduction
SCALEPACK data scaling