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, 14% PEG 3350, 0.14M NH4F, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 137.56 α = 90
b = 49.92 β = 93.68
c = 34.24 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 ADSC QUANTUM 4 TOROIDAL MIRROR 2008-02-25
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2

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
1.79 40 100.0 0.117 -- -- 7.4 -- 21929 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)
1.79 1.82 100.0 0.536 -- -- 7.2 1072

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 1.791 34.32 0.0 1.36 21923 21923 1114 99.84 -- 0.1441 0.1417 0.1876 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 1.791 1.8722 -- 147 2527 0.1778 0.2389 -- 99.0
X Ray Diffraction 1.8722 1.9709 -- 118 2612 0.1607 0.2136 -- 100.0
X Ray Diffraction 1.9709 2.0943 -- 136 2572 0.1485 0.2132 -- 100.0
X Ray Diffraction 2.0943 2.256 -- 134 2621 0.1398 0.1852 -- 100.0
X Ray Diffraction 2.256 2.483 -- 147 2583 0.1463 0.2019 -- 100.0
X Ray Diffraction 2.483 2.8421 -- 135 2616 0.1446 0.193 -- 100.0
X Ray Diffraction 2.8421 3.5802 -- 127 2630 0.1283 0.1889 -- 100.0
X Ray Diffraction 3.5802 34.3259 -- 170 2648 0.1316 0.155 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.1195
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_chiral_restr 0.078
f_plane_restr 0.005
f_angle_d 1.146
f_dihedral_angle_d 17.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1543
Nucleic Acid Atoms 225
Heterogen Atoms 69
Solvent Atoms 335

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
DNA data collection
HKL-2000 data reduction
HKL-2000 data scaling