X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 290.0
Details 40 mM sodium cacodylate (pH 7.0), 12 mM spermine, 80 mM KCl, 10% (v/v) MPD equilibrated against 35% MPD with oligo concentration of 1 mM, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.87 α = 90
b = 25.36 β = 110.57
c = 37.37 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
IMAGE PLATE MARRESEARCH mirrors 2001-07-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.073 EMBL/DESY, HAMBURG X31

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
2.35 30 96.3 0.064 -- -- -- 4339 2387 4.0 2.0 --
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)
2.35 2.43 97.3 0.267 -- -- -- --

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
-- 2.35 34.92 -- -- -- 2286 104 96.41 -- 0.22841 0.22639 0.26779 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 2.35 2.411 -- 7 157 0.297 0.393 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.349
Anisotropic B[1][1] -2.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] 3.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.41
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.157
r_nbd_other 0.329
r_nbd_refined 0.268
r_gen_planes_refined 0.033
r_chiral_restr 0.518
r_angle_other_deg 1.463
r_angle_refined_deg 2.195
r_bond_other_d 0.002
r_bond_refined_d 0.067
r_xyhbond_nbd_refined 0.523
r_xyhbond_nbd_other 0.025
r_symmetry_vdw_refined 0.155
r_symmetry_vdw_other 0.213
r_symmetry_hbond_refined 0.204
Coordinate Error
Parameter Value
Number Disordered Residues 0.0
Occupancy Sum Hydrogen 0.0
Occupancy Sum Non Hydrogen 426.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 404
Heterogen Atoms 0
Solvent Atoms 43

Software

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