X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.5
Details 365mM ammonium acetate, 100mM trisodium citrate, 18.5% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.68 α = 90
b = 85.68 β = 90
c = 108.81 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2009-05-12
Diffraction Radiation
Monochromator Protocol
single crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1

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
2.28 37.1 81.4 0.061 -- -- 4.3 40821 33227 0.0 0.0 42.2
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)
2.28 2.38 35.3 0.254 -- 5.03 1.43 1751

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 2.401 35.117 -- 1.96 -- 29669 1499 84.93 -- 0.2 0.198 0.239 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 2.4011 2.4869 1101 55 1101 0.2424 0.3286 -- 33.0
X Ray Diffraction 2.4869 2.5864 1658 90 1658 0.2774 0.3403 -- 51.0
X Ray Diffraction 2.5864 2.7041 2507 128 2507 0.2706 0.3459 -- 75.0
X Ray Diffraction 2.7041 2.8466 3058 173 3058 0.2631 0.3379 -- 93.0
X Ray Diffraction 2.8466 3.0249 3310 179 3310 0.2523 0.2924 -- 100.0
X Ray Diffraction 3.0249 3.2583 3277 176 3277 0.2204 0.3027 -- 100.0
X Ray Diffraction 3.2583 3.5859 3314 190 3314 0.1992 0.2535 -- 100.0
X Ray Diffraction 3.5859 4.1041 3317 186 3317 0.1717 0.2107 -- 100.0
X Ray Diffraction 4.1041 5.168 3301 176 3301 0.1551 0.1701 -- 100.0
X Ray Diffraction 5.168 35.1211 3327 146 3327 0.1681 0.1746 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.743
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.06
f_dihedral_angle_d 18.229
f_angle_d 1.304
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3846
Nucleic Acid Atoms 761
Heterogen Atoms 0
Solvent Atoms 150

Software

Computing
Computing Package Purpose
Blue-ice Data Collection
HKL-2000 Data Reduction (intensity integration)
XPREP Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_222) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_222) refinement
PHASER model building
Blue-ice data collection