X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 289.0
Details 0.1 M PCB buffer, 20 % v/v PEG 1500, 10 mM spermidine , pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.02 α = 90
b = 48.02 β = 90
c = 218.35 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2008-11-06
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.933000 ESRF ID14-4

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
2.4 38.86 95.6 0.048 -- -- -- -- 21045 -- -3.0 59.528
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)
2.4 2.5 85.4 0.542 -- 1.46 -- --

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 2.4 38.86 -- 0.0 21045 21041 1069 95.8 -- 0.2002 0.1972 0.2599 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 2.4 2.462 -- 62 1211 0.292 0.374 -- 82.45
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.385
Anisotropic B[1][1] 0.42
Anisotropic B[1][2] 0.42
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.37
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_dihedral_angle_1_deg 5.816
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_bond_refined_d 0.011
r_dihedral_angle_4_deg 19.325
r_angle_other_deg 1.168
r_dihedral_angle_3_deg 18.365
r_chiral_restr 0.092
r_angle_refined_deg 1.522
r_dihedral_angle_2_deg 36.805
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2458
Nucleic Acid Atoms 2050
Heterogen Atoms 0
Solvent Atoms 23

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
DNA data collection