X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details Reservoir: 25% PEG 10000, 0.2M imidazole malate. Cryoprotectant: 27% PEG 8000, 15% MPEG 550, 10% glycerol, .01M hydroxamic acid, 90mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.58 α = 90
b = 63.39 β = 90
c = 36.9 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r bent cylindrical mirror 2009-02-23
Diffraction Radiation
Monochromator Protocol
horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.979300 ESRF ID23-1

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
1.15 50 98.6 0.091 0.084 -- 6.9 58830 58014 0.0 0.0 13.934
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)
1.15 1.22 96.5 1.3 1.2 2.3 6.73 --

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 1.15 32.599 -- 1.99 58014 57994 2900 98.69 -- 0.1343 0.1333 0.1545 --
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 1.15 1.1689 -- 124 2342 0.312 0.3186 -- 91.0
X Ray Diffraction 1.1689 1.189 -- 139 2641 0.252 0.232 -- 100.0
X Ray Diffraction 1.189 1.2107 -- 137 2613 0.2202 0.2341 -- 100.0
X Ray Diffraction 1.2107 1.234 -- 138 2638 0.2176 0.2582 -- 100.0
X Ray Diffraction 1.234 1.2591 -- 137 2593 0.1946 0.2375 -- 100.0
X Ray Diffraction 1.2591 1.2865 -- 139 2649 0.1761 0.2652 -- 100.0
X Ray Diffraction 1.2865 1.3164 -- 139 2631 0.1642 0.1911 -- 100.0
X Ray Diffraction 1.3164 1.3494 -- 137 2606 0.1386 0.1624 -- 100.0
X Ray Diffraction 1.3494 1.3859 -- 139 2638 0.1261 0.1409 -- 100.0
X Ray Diffraction 1.3859 1.4266 -- 139 2648 0.1182 0.1495 -- 100.0
X Ray Diffraction 1.4266 1.4727 -- 138 2628 0.1081 0.1307 -- 100.0
X Ray Diffraction 1.4727 1.5253 -- 139 2634 0.1065 0.1338 -- 100.0
X Ray Diffraction 1.5253 1.5864 -- 139 2649 0.0982 0.126 -- 100.0
X Ray Diffraction 1.5864 1.6586 -- 140 2654 0.1016 0.1416 -- 100.0
X Ray Diffraction 1.6586 1.746 -- 140 2664 0.1061 0.1249 -- 100.0
X Ray Diffraction 1.746 1.8554 -- 139 2636 0.1091 0.1279 -- 100.0
X Ray Diffraction 1.8554 1.9986 -- 141 2670 0.1108 0.1214 -- 100.0
X Ray Diffraction 1.9986 2.1997 -- 141 2695 0.1119 0.1236 -- 100.0
X Ray Diffraction 2.1997 2.5179 -- 142 2684 0.1189 0.1331 -- 100.0
X Ray Diffraction 2.5179 3.1719 -- 144 2732 0.1276 0.1492 -- 99.0
X Ray Diffraction 3.1719 32.6125 -- 129 2449 0.1504 0.1702 -- 85.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.112
f_dihedral_angle_d 15.377
f_angle_d 1.5
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 303

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
MOLREP model building
DNA data collection