X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 308.0
Details 80 mM MgCl2, 1.0 M Na tartrate, 50 mM Tris.HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 308 K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.25 α = 90
b = 116.9 β = 90
c = 170.5 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
CCD MARMOSAIC 300 mm CCD -- 2009-03-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C

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
3.2 50 95.2 0.12 -- -- 4.9 -- 34970 -1.0 -- 95.75
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)
3.2 3.31 88.9 0.412 -- 1.5 3.5 3220

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 3.211 37.68 -- 0.13 -- 34940 1743 94.41 -- 0.229 0.226 0.273 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 3.211 3.306 -- 128 2257 0.343 0.414 -- 78.0
X Ray Diffraction 3.306 3.412 -- 154 2620 0.298 0.376 -- 91.0
X Ray Diffraction 3.412 3.534 -- 117 2701 0.262 0.346 -- 93.0
X Ray Diffraction 3.534 3.675 -- 131 2712 0.234 0.28 -- 94.0
X Ray Diffraction 3.675 3.842 -- 153 2769 0.209 0.302 -- 95.0
X Ray Diffraction 3.842 4.045 -- 133 2768 0.199 0.278 -- 95.0
X Ray Diffraction 4.045 4.298 -- 140 2812 0.193 0.244 -- 97.0
X Ray Diffraction 4.298 4.629 -- 158 2860 0.173 0.237 -- 98.0
X Ray Diffraction 4.629 5.094 -- 164 2843 0.183 0.243 -- 98.0
X Ray Diffraction 5.094 5.829 -- 162 2891 0.195 0.254 -- 98.0
X Ray Diffraction 5.829 7.335 -- 150 2949 0.216 0.24 -- 99.0
X Ray Diffraction 7.335 37.683 -- 153 3015 0.219 0.238 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 97.522
Anisotropic B[1][1] 3.626
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.149
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.775
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_dihedral_angle_d 16.216
f_plane_restr 0.008
f_angle_d 1.111
f_chiral_restr 0.071
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9513
Nucleic Acid Atoms 1108
Heterogen Atoms 16
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing