X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Temperature 285.0
Details 100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.22 α = 90
b = 123.97 β = 103.68
c = 78.31 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 285
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F COMPOUND REFRACTIVE LENSES 2014-08-10
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 -- Diamond I04

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 76.1 99.0 0.072 -- -- 3.5 -- 17755 -- -3.0 85.71
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)
3.0 3.1 95.3 0.4869 -- 2.05 3.4 --

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 3.03 76.1 -- 0.0 -- 16797 957 98.8 -- 0.225 0.222 0.27 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 3.03 3.11 -- 68 1161 0.372 0.382 -- 93.75
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.9
Anisotropic B[1][1] 8.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.36
Anisotropic B[2][2] 3.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.58
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 32.454
r_angle_other_deg 0.69
r_dihedral_angle_3_deg 13.457
r_bond_other_d 0.001
r_bond_refined_d 0.004
r_scbond_other 1.776
r_dihedral_angle_4_deg 11.294
r_mcbond_it 1.893
r_scangle_other 3.087
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
r_angle_refined_deg 0.84
r_mcbond_other 1.889
r_dihedral_angle_1_deg 4.563
r_chiral_restr 0.049
r_long_range_B_other 5.249
r_mcangle_other 3.254
r_mcangle_it 3.254
r_long_range_B_refined 5.25
r_scbond_it 1.777
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3623
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 0

Software

Software
Software Name Purpose
EDNA data collection
PHASER phasing
REFMAC refinement version: 5.8.0073
XDS data reduction
SCALA data scaling