X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Method
pH 9
Temperature 293.0
Details Protein solution (20mg/ml protein in 0.02m Tris-HCl ph9.0) mixed with mother liquor (3.2m ammonium sulphate, 0.05m tris-hcl, ph9.0) for final concentrations of 2.5m ammonium sulphate, Batch Method, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.93 α = 90
b = 46.96 β = 90
c = 89.5 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
IMAGE PLATE RIGAKU RAXIS -- 2009-04-10
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.68 41.59 98.9 0.041 -- -- 3.71 -- 19145 -- 3.0 --
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)
1.68 1.74 94.7 0.159 -- 7.0 3.2 1788

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 1.68 22.711 -- 1.0 -- 19099 1909 98.72 -- 0.1689 0.1658 0.196 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 1.68 1.7219 -- 122 1106 0.155 0.2121 -- 92.0
X Ray Diffraction 1.7219 1.7684 -- 133 1194 0.1505 0.2003 -- 97.0
X Ray Diffraction 1.7684 1.8205 -- 135 1213 0.1391 0.1871 -- 99.0
X Ray Diffraction 1.8205 1.8792 -- 133 1200 0.1497 0.1842 -- 98.0
X Ray Diffraction 1.8792 1.9463 -- 134 1201 0.1527 0.1956 -- 98.0
X Ray Diffraction 1.9463 2.0242 -- 136 1220 0.1476 0.2103 -- 100.0
X Ray Diffraction 2.0242 2.1163 -- 135 1225 0.1403 0.1815 -- 99.0
X Ray Diffraction 2.1163 2.2278 -- 136 1223 0.1291 0.161 -- 100.0
X Ray Diffraction 2.2278 2.3672 -- 138 1245 0.122 0.1603 -- 100.0
X Ray Diffraction 2.3672 2.5497 -- 136 1233 0.1268 0.1454 -- 100.0
X Ray Diffraction 2.5497 2.8059 -- 139 1249 0.1519 0.1823 -- 100.0
X Ray Diffraction 2.8059 3.211 -- 140 1263 0.1656 0.2166 -- 100.0
X Ray Diffraction 3.211 4.0418 -- 141 1269 0.1416 0.1758 -- 100.0
X Ray Diffraction 4.0418 22.7135 -- 151 1349 0.173 0.1692 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.653
Anisotropic B[1][1] 1.2507
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.9086
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.342
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.242
f_chiral_restr 0.064
f_plane_restr 0.005
f_dihedral_angle_d 13.89
f_bond_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1229
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 233

Software

Software
Software Name Purpose
PHENIX refinement version: 1.6.1_357
CNS refinement
d*TREK data scaling
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
d*TREK data reduction
CNS phasing