X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 1:2.4 PROTEIN/DNA RATIO, 16% PEG 3350, 0.18M NH4F, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 137.63 α = 90
b = 50.3 β = 93.46
c = 34.01 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Pt coated Si mirror in Kirkpatrick-Baez geometry 2009-02-17
Diffraction Radiation
Monochromator Protocol
SILICON (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2

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
2.1 50 96.6 0.082 -- -- 6.2 -- 13264 0.0 0.0 --
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)
2.1 2.14 83.6 0.255 -- -- 3.3 --

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 2.1 47.235 -- 1.34 13262 13262 667 96.25 -- 0.1648 0.1614 0.2294 --
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 2.1 2.258 -- 101 2293 0.1808 0.2416 -- 87.0
X Ray Diffraction 2.258 2.4852 -- 156 2460 0.1786 0.2581 -- 97.0
X Ray Diffraction 2.4852 2.8448 -- 143 2581 0.1839 0.2552 -- 99.0
X Ray Diffraction 2.8448 3.5839 -- 138 2591 0.1604 0.2253 -- 99.0
X Ray Diffraction 3.5839 47.2472 -- 129 2670 0.1415 0.2031 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.025
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.445
f_angle_d 1.21
f_plane_restr 0.006
f_bond_d 0.007
f_chiral_restr 0.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1535
Nucleic Acid Atoms 221
Heterogen Atoms 29
Solvent Atoms 164

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: dev_1405
PDB_EXTRACT data extraction version: 3.11
DNA data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing