X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 281.0
Details Hanging drop vapor diffusion at 4C, with initial concentration in drop of 0.13 mM DNA, 0.33 mM Hin, 46 mMTris (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 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.75 α = 90
b = 81.14 β = 90
c = 44.6 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
2.4 30 85.35 -- 0.079 -- 26.0 -- 5435 -- 0.0 47.0
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)
2.4 2.51 43.76 -- 0.27 2.6 1.91 --

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 2.4 30.0 -- 0.0 -- 5435 536 85.4 -- 0.223 0.223 0.278 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 2.51 -- 39 337 0.424 0.421 -- 43.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC_FIXED_ISOTROPIC
Mean Isotropic B 40.0
Anisotropic B[1][1] 14.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -19.21
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 12.6
c_scbond_it 9.8
c_mcangle_it 8.2
c_mcbond_it 5.9
c_improper_angle_d 1.846
c_bond_d 0.0087
c_angle_deg 1.819
c_dihedral_angle_d 17.88
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.57
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.52
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 358
Nucleic Acid Atoms 569
Heterogen Atoms 16
Solvent Atoms 7

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
SOLVE model building