X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.6
Temperature 281.0
Details 200 nL 7 mg/mL protein + 200 nL reservoir (2.8 M ammonium sulfate, 100 mM Tris, pH 8.6)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.38 α = 90
b = 41.6 β = 104.21
c = 72.2 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2017-07-06
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1

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
1.21 41.6 97.9 0.094 -- -- 7.2 -- 73224 -- -- --
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)
1.21 1.23 91.2 0.704 -- -- 6.4 --

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 1.21 41.6 -- -- -- 69692 3513 97.7 -- 0.1333 0.1321 0.15721 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 1.208 1.239 -- 249 4847 0.249 0.308 -- 92.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.171
Anisotropic B[1][1] -0.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.04
Anisotropic B[2][2] 0.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.29
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.049
r_long_range_B_refined 2.377
r_gen_planes_refined 0.008
r_bond_refined_d 0.009
r_mcangle_other 1.003
r_scbond_other 1.049
r_rigid_bond_restr 8.949
r_sphericity_free 23.094
r_sphericity_bonded 7.781
r_gen_planes_other 0.003
r_dihedral_angle_4_deg 21.548
r_mcbond_it 0.74
r_long_range_B_other 2.377
r_angle_other_deg 1.032
r_dihedral_angle_1_deg 6.256
r_mcangle_it 0.99
r_angle_refined_deg 1.44
r_bond_other_d 0.002
r_mcbond_other 0.743
r_dihedral_angle_2_deg 39.653
r_scangle_other 1.211
r_chiral_restr 0.092
r_dihedral_angle_3_deg 11.149
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2064
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 363

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0218
ADDREF data reduction
Aimless data scaling
PHASER phasing