X-RAY DIFFRACTION Experimental Data & Validation


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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_dihedral_angle_d 17.027
f_plane_restr 0.005
f_chiral_restr 0.078
f_angle_d 1.146
f_bond_d 0.006
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

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: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
MOLREP molecular replacement
HKL data reduction