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_plane_restr 0.006
f_chiral_restr 0.078
f_dihedral_angle_d 18.445
f_angle_d 1.21
f_bond_d 0.007
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

Computing
Computing Package Purpose
DNA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: dev_1405) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction