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 = 121.68 α = 90
b = 121.68 β = 90
c = 179.39 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
3.5 36.1 -- -- -- -- -- -- 34810 -- -- 176.35

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 4.001 36.1 -- 1.96 -- 24916 2521 99.38 -- 0.2635 0.2581 0.3131 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 4.0006 4.0774 -- 142 1289 0.303 0.385 -- 100.0
X Ray Diffraction 4.0774 4.1605 -- 129 1249 0.2812 0.3338 -- 100.0
X Ray Diffraction 4.1605 4.2508 -- 140 1265 0.266 0.3677 -- 100.0
X Ray Diffraction 4.2508 4.3496 -- 145 1261 0.2707 0.307 -- 100.0
X Ray Diffraction 4.3496 4.4581 -- 123 1228 0.2498 0.3054 -- 100.0
X Ray Diffraction 4.4581 4.5785 -- 141 1249 0.2327 0.2912 -- 100.0
X Ray Diffraction 4.5785 4.7129 -- 157 1236 0.2347 0.3082 -- 100.0
X Ray Diffraction 4.7129 4.8647 -- 148 1266 0.2288 0.2994 -- 100.0
X Ray Diffraction 4.8647 5.0381 -- 151 1257 0.2446 0.3047 -- 100.0
X Ray Diffraction 5.0381 5.2392 -- 118 1229 0.2466 0.2921 -- 100.0
X Ray Diffraction 5.2392 5.4769 -- 166 1238 0.2759 0.3335 -- 100.0
X Ray Diffraction 5.4769 5.7646 -- 130 1266 0.2828 0.3468 -- 100.0
X Ray Diffraction 5.7646 6.1241 -- 154 1219 0.2841 0.3422 -- 100.0
X Ray Diffraction 6.1241 6.5943 -- 151 1267 0.2898 0.3776 -- 100.0
X Ray Diffraction 6.5943 7.2531 -- 131 1248 0.2712 0.3314 -- 100.0
X Ray Diffraction 7.2531 8.2915 -- 153 1227 0.2305 0.2593 -- 100.0
X Ray Diffraction 8.2915 10.4048 -- 137 1269 0.1832 0.2075 -- 100.0
X Ray Diffraction 10.4048 36.1011 -- 105 1132 0.295 0.3691 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 202.667
Anisotropic B[1][1] -17.079
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -17.079
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -31.577
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.381
f_plane_restr 0.008
f_chiral_restr 0.051
f_angle_d 1.7
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6917
Nucleic Acid Atoms 1374
Heterogen Atoms 50
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