X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Temperature 292.0
Details A 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL,12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR ZN2+ SOAKING A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM ZNCL2 FOR ONE WEEK.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 17.79 α = 90
b = 30.91 β = 90
c = 44.2 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
FLAT PANEL MAR555 FLAT PANEL -- 2010-12-02
Diffraction Radiation
Monochromator Protocol
SI 111 CHANNEL 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
0.85 17.98 87.9 0.036 -- -- 3.02 -- 36512 -- -3.0 8.109
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)
0.85 0.9 63.8 0.222 -- 3.11 1.77 --

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 0.85 17.976 -- -- 36512 -- 1004 87.9 0.092 0.092 -- 0.113 RANDOM
RMS Deviations
Key Refinement Restraint Deviation
s_approx_iso_adps 0.076
s_similar_adp_cmpnt 0.033
s_rigid_bond_adp_cmpnt 0.025
s_anti_bump_dis_restr 0.123
s_non_zero_chiral_vol 0.0
s_zero_chiral_vol 0.0
s_from_restr_planes 0.0
s_similar_dist 0.0
s_angle_d 0.059
s_bond_d 0.027
Coordinate Error
Parameter Value
Number Disordered Residues 6.0
Occupancy Sum Hydrogen 144.6
Occupancy Sum Non Hydrogen 313.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 240
Heterogen Atoms 17
Solvent Atoms 75

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
SHELXL-97 Structure Refinement
Software
Software Name Purpose
SHELXL-97 refinement
PHASER model building
MAR345dtb data collection