X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.5 mM duplex, 1mM drug-peptide adduct, 20 mM NaCacodylate, 100 mM MgCl2, 45% MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.47 α = 90
b = 68.36 β = 90
c = 77.36 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 -- EMBL/DESY, HAMBURG X11

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
2.7 30 91.2 0.054 -- -- 8.8 -- 12155 -- 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)
2.7 3.2 90.3 0.223 -- -- 1.64 --

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 2.7 20.0 -- -- -- 8086 921 89.05 -- 0.22476 0.22005 0.26607 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 2.7 2.769 -- 62 575 0.343 0.492 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.54
Anisotropic B[1][1] -4.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.87
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.129
r_gen_planes_refined 0.009
r_chiral_restr 0.099
r_dihedral_angle_3_deg 31.341
r_dihedral_angle_1_deg 3.978
r_angle_refined_deg 2.409
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.128
r_symmetry_vdw_refined 0.119
r_symmetry_hbond_refined 0.152
r_mcbond_it 0.457
r_mcangle_it 1.136
r_scbond_it 1.37
r_scangle_it 1.875
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 48
Nucleic Acid Atoms 2897
Heterogen Atoms 7
Solvent Atoms 103

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMORE model building