X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details PEG 3350, Bis-Tris, ammonium sulfate, glycerol (cryo-protectant)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 161.42 α = 90
b = 161.42 β = 90
c = 140.05 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-07-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 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
2.24 52.89 100.0 0.438 -- -- 21.6 -- 51846 -- -- --
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)
2.24 2.31 100.0 3.135 -- 1.4 19.7 4420

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 2.24 52.89 -- 0.0 -- 49268 2548 99.97 -- 0.219 0.2169 0.2589 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 2.244 2.302 -- 184 3597 0.385 0.378 -- 100.0
X Ray Diffraction 2.302 2.365 -- 170 3462 0.363 0.368 -- 100.0
X Ray Diffraction 2.365 2.434 -- 155 3423 0.342 0.397 -- 100.0
X Ray Diffraction 2.434 2.508 -- 172 3296 0.31 0.334 -- 99.971
X Ray Diffraction 2.508 2.59 -- 165 3196 0.296 0.349 -- 99.97
X Ray Diffraction 2.59 2.681 -- 160 3100 0.265 0.294 -- 100.0
X Ray Diffraction 2.681 2.782 -- 160 2999 0.262 0.343 -- 100.0
X Ray Diffraction 2.782 2.895 -- 164 2884 0.247 0.334 -- 100.0
X Ray Diffraction 2.895 3.024 -- 133 2781 0.234 0.307 -- 100.0
X Ray Diffraction 3.024 3.171 -- 133 2681 0.242 0.298 -- 100.0
X Ray Diffraction 3.171 3.341 -- 119 2544 0.214 0.272 -- 100.0
X Ray Diffraction 3.341 3.543 -- 131 2399 0.194 0.234 -- 100.0
X Ray Diffraction 3.543 3.787 -- 119 2281 0.185 0.207 -- 100.0
X Ray Diffraction 3.787 4.088 -- 121 2106 0.159 0.235 -- 99.955
X Ray Diffraction 4.088 4.476 -- 110 1967 0.129 0.166 -- 100.0
X Ray Diffraction 4.476 5.0 -- 89 1803 0.125 0.143 -- 100.0
X Ray Diffraction 5.0 5.765 -- 94 1593 0.141 0.213 -- 100.0
X Ray Diffraction 5.765 7.039 -- 92 1356 0.165 0.181 -- 100.0
X Ray Diffraction 7.039 9.868 -- 47 1101 0.137 0.183 -- 99.826
X Ray Diffraction 9.868 52.89 -- 30 698 0.219 0.322 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.56
Anisotropic B[1][1] 1.55
Anisotropic B[1][2] 0.78
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.04
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.104
r_dihedral_angle_2_deg 41.085
r_mcbond_other 1.219
r_bond_refined_d 0.006
r_mcbond_it 1.219
r_mcangle_it 2.062
r_dihedral_angle_3_deg 14.217
r_dihedral_angle_4_deg 14.521
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 5.785
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_chiral_restr 0.059
r_angle_other_deg 0.725
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6492
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 182

Software

Software
Software Name Purpose
REFMAC refinement version: refmac_5.8.0073
PHASER phasing version: 2.5.6
Aimless data scaling version: 0.3.6
iMOSFLM data reduction version: 7.1.1
PDB_EXTRACT data extraction version: 3.15