X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 280.0
Details Hanging drop vapor diffusion at 4C, with initial concentration in drop of 0.13 mM DNA, 0.33 mM Hin, 46 mM Tris (pH 8.5), 46 mM CaCl2, 63 mM NaCl, 11.6% v/v PEG400, and 2.03 mM Na cacodylate. Reservoir solution contains 100 mM Tris (pH 8.5), 100 mM CaCl2, 100 mM NaCl, and 25% PEG400. Concentration of PEG400 in reservoir solution was increased in 5% increments to 35%., VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.8 α = 90
b = 82.12 β = 90
c = 45.23 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 1999-06-01
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C -- NSLS X12C

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
2.3 30 89.55 -- 0.067 -- 43.0 -- 6695 -- 0.0 54.0
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)
2.3 2.4 55.33 -- 0.192 6.34 -- --

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
MIRAS 2.3 30.0 -- 0.0 -- 6695 681 89.55 -- 0.238 0.238 0.2807 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 2.3 2.4 -- 61 504 0.356 0.38 -- 55.33
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC_FIXED_ISOTROPIC
Mean Isotropic B 52.0
Anisotropic B[1][1] 18.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 12.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -31.13
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 3.0
c_bond_d 0.011
c_dihedral_angle_d 18.16
c_mcangle_it 4.9
c_angle_deg 1.887
c_scangle_it 7.6
c_improper_angle_d 1.976
c_mcbond_it 2.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.59
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.5
Luzzati Sigma A (R-Free Set) 0.54
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 360
Nucleic Acid Atoms 575
Heterogen Atoms 9
Solvent Atoms 10

Software

Software
Software Name Purpose
SOLVE phasing
CNS refinement
DENZO data reduction
SCALEPACK data scaling