X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details 50mM Na cacodylate, 100mM Ammonium acetate, 15mM Magnesium acetate, 7.5% isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.6 α = 90
b = 121.6 β = 90
c = 178.7 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-06-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.97 DIAMOND I03

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 34.07 -- -- -- -- -- -- 44580 -- -- 178.14

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 4.0 34.066 -- 1.98 -- 24685 2492 98.92 -- 0.2441 0.239 0.2892 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 4.0001 4.0769 -- 149 1279 0.2687 0.3108 -- 100.0
X Ray Diffraction 4.0769 4.16 -- 160 1202 0.2509 0.314 -- 100.0
X Ray Diffraction 4.16 4.2503 -- 133 1264 0.2303 0.3015 -- 100.0
X Ray Diffraction 4.2503 4.349 -- 151 1235 0.2213 0.2674 -- 100.0
X Ray Diffraction 4.349 4.4575 -- 133 1246 0.2205 0.2787 -- 100.0
X Ray Diffraction 4.4575 4.5778 -- 136 1246 0.2108 0.2821 -- 100.0
X Ray Diffraction 4.5778 4.7121 -- 142 1261 0.2132 0.2594 -- 100.0
X Ray Diffraction 4.7121 4.8638 -- 115 1276 0.1976 0.234 -- 100.0
X Ray Diffraction 4.8638 5.0371 -- 153 1235 0.2172 0.2617 -- 100.0
X Ray Diffraction 5.0371 5.2381 -- 140 1221 0.2346 0.2893 -- 100.0
X Ray Diffraction 5.2381 5.4756 -- 139 1235 0.2508 0.298 -- 100.0
X Ray Diffraction 5.4756 5.763 -- 132 1272 0.2699 0.3613 -- 100.0
X Ray Diffraction 5.763 6.1221 -- 152 1225 0.287 0.3774 -- 100.0
X Ray Diffraction 6.1221 6.5916 -- 151 1239 0.2896 0.3195 -- 100.0
X Ray Diffraction 6.5916 7.2492 -- 131 1260 0.2472 0.3129 -- 100.0
X Ray Diffraction 7.2492 8.285 -- 127 1233 0.2168 0.2318 -- 100.0
X Ray Diffraction 8.285 10.3888 -- 137 1253 0.1782 0.2351 -- 99.0
X Ray Diffraction 10.3888 34.0668 -- 111 1011 0.2632 0.2986 -- 81.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 198.798
Anisotropic B[1][1] -7.561
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.561
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.421
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.918
f_plane_restr 0.012
f_chiral_restr 0.051
f_angle_d 1.208
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7020
Nucleic Acid Atoms 1374
Heterogen Atoms 58
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine) refinement
Phaser model building