X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 183.59 α = 90
b = 248.97 β = 90
c = 122.29 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-11-21
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2

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
2.9 50 95.8 -- 0.185 -- 3.9 457504 118133 0.0 0.0 50.8
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)
2.9 2.98 93.5 -- 0.537 2.1 3.3 --

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 2.902 50.0 -- 1.34 118133 118084 5918 95.03 -- 0.2082 0.2055 0.2584 --
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 2.9024 2.9354 -- 188 3418 0.305 0.3606 -- 88.0
X Ray Diffraction 2.9354 2.9699 -- 197 3781 0.2907 0.331 -- 97.0
X Ray Diffraction 2.9699 3.0061 -- 207 3754 0.2813 0.347 -- 97.0
X Ray Diffraction 3.0061 3.0442 -- 220 3772 0.2785 0.3503 -- 97.0
X Ray Diffraction 3.0442 3.0843 -- 179 3780 0.2706 0.3337 -- 97.0
X Ray Diffraction 3.0843 3.1265 -- 191 3802 0.2675 0.3495 -- 97.0
X Ray Diffraction 3.1265 3.1712 -- 179 3759 0.2622 0.3192 -- 97.0
X Ray Diffraction 3.1712 3.2185 -- 196 3823 0.2509 0.3607 -- 97.0
X Ray Diffraction 3.2185 3.2688 -- 223 3718 0.2428 0.2842 -- 97.0
X Ray Diffraction 3.2688 3.3224 -- 209 3758 0.2385 0.3439 -- 97.0
X Ray Diffraction 3.3224 3.3797 -- 216 3755 0.2306 0.2975 -- 97.0
X Ray Diffraction 3.3797 3.4412 -- 202 3759 0.2227 0.2848 -- 96.0
X Ray Diffraction 3.4412 3.5074 -- 196 3777 0.2132 0.2898 -- 96.0
X Ray Diffraction 3.5074 3.579 -- 191 3741 0.2008 0.2339 -- 96.0
X Ray Diffraction 3.579 3.6568 -- 217 3726 0.1995 0.26 -- 95.0
X Ray Diffraction 3.6568 3.7419 -- 205 3758 0.1985 0.2569 -- 96.0
X Ray Diffraction 3.7419 3.8354 -- 200 3754 0.1928 0.2367 -- 96.0
X Ray Diffraction 3.8354 3.9391 -- 196 3730 0.179 0.2121 -- 96.0
X Ray Diffraction 3.9391 4.0551 -- 203 3736 0.1806 0.25 -- 95.0
X Ray Diffraction 4.0551 4.186 -- 189 3748 0.1659 0.219 -- 95.0
X Ray Diffraction 4.186 4.3356 -- 188 3729 0.1682 0.2203 -- 95.0
X Ray Diffraction 4.3356 4.5092 -- 184 3757 0.1695 0.2111 -- 95.0
X Ray Diffraction 4.5092 4.7144 -- 213 3720 0.1685 0.215 -- 95.0
X Ray Diffraction 4.7144 4.963 -- 191 3735 0.1715 0.23 -- 95.0
X Ray Diffraction 4.963 5.2739 -- 198 3744 0.1834 0.2281 -- 94.0
X Ray Diffraction 5.2739 5.6812 -- 186 3706 0.1946 0.2437 -- 93.0
X Ray Diffraction 5.6812 6.2529 -- 208 3718 0.2031 0.244 -- 93.0
X Ray Diffraction 6.2529 7.1577 -- 189 3716 0.2002 0.2257 -- 93.0
X Ray Diffraction 7.1577 9.0178 -- 169 3736 0.164 0.1839 -- 92.0
X Ray Diffraction 9.0178 147.953 -- 188 3756 0.1992 0.2146 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -12.1402
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.0761
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -19.2864
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.06
f_dihedral_angle_d 15.622
f_angle_d 0.862
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 39092
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 45

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
Phaser model building
ADSC version: Quantum data collection