X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Lipidic Cubic Phase
pH 6
Temperature 293.0
Details 25-28% (v/v) PEG 400, 0.12 to 0.2 M NaCl, 100 mM MES buffer at pH 6.0, 1 mM DIPP-NH2 and 5% (v/v) of either one of the following additives: 30% glycerol, 1.0 M glycine or 0.01M L-glutathione reduced/0.01M L-glutathione oxidized, Lipidic cubic phase, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.55 α = 90
b = 86.12 β = 92.21
c = 94.68 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors 2013-12-08
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0330 APS 23-ID-B

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
3.28 94.61 96.3 0.173 -- -- 4.3 -- 18862 -- -- --
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)
3.3 3.51 97.3 0.875 -- 1.9 4.4 --

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 3.28 94.61 -- -- -- 17904 958 94.68 -- 0.24067 0.23891 0.27296 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 3.282 3.367 -- 51 1043 0.334 0.377 -- 75.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 90.825
Anisotropic B[1][1] -3.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.31
Anisotropic B[2][2] 1.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.98
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_gen_planes_other 0.002
r_scangle_other 5.348
r_long_range_B_refined 8.432
r_bond_refined_d 0.007
r_dihedral_angle_3_deg 17.824
r_bond_other_d 0.003
r_dihedral_angle_4_deg 18.121
r_long_range_B_other 8.431
r_mcangle_other 5.36
r_scbond_other 3.206
r_chiral_restr 0.056
r_mcbond_other 3.29
r_angle_other_deg 0.982
r_angle_refined_deg 1.146
r_dihedral_angle_2_deg 39.741
r_mcangle_it 5.36
r_mcbond_it 3.296
r_scbond_it 3.206
r_dihedral_angle_1_deg 5.315
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5920
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 1

Software

Software
Software Name Purpose
Blu-Ice data collection version: Ice
PHASER phasing
REFMAC refinement version: 5.8.0049
HKL-2000 data reduction
HKL-2000 data scaling