X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Temperature 293.15
Details 100 mM sodium acetate pH 5.4 and 18.5 % PEG3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.14 α = 90
b = 55.14 β = 90
c = 105.51 γ = 90
Symmetry
Space Group I 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M -- 2015-05-01
Diffraction Radiation
Monochromator Protocol
single crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96769 ESRF MASSIF-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
2.05 48.87 100.0 0.043 -- -- 6.6 -- 9899 -- -- --
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)
2.05 2.11 100.0 0.544 -- 2.9 6.6 --

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 2.05 48.87 -- -- -- 9368 517 99.97 -- 0.18484 0.18268 0.22341 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 2.05 2.103 -- 39 674 0.255 0.303 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.638
Anisotropic B[1][1] 0.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.69
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_dihedral_angle_1_deg 6.1
r_scbond_it 3.95
r_mcangle_other 3.808
r_gen_planes_refined 0.005
r_long_range_B_refined 7.303
r_long_range_B_other 7.313
r_mcangle_it 3.804
r_scbond_other 3.947
r_angle_other_deg 0.904
r_chiral_restr 0.081
r_mcbond_other 3.014
r_dihedral_angle_3_deg 14.185
r_mcbond_it 3.035
r_angle_refined_deg 1.441
r_scangle_other 6.165
r_dihedral_angle_4_deg 13.893
r_dihedral_angle_2_deg 38.29
r_gen_planes_other 0.001
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1332
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 3

Software

Software
Software Name Purpose
XDS data reduction
PHASER phasing
REFMAC refinement version: 5.8.0155
XDS data scaling