X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 30 % PEG 1000, 270 mM CH3COONH4, 3% 6-aminohexanoic acid (ACA). 1.5 uL 5 mg/mL Stock + 1.5 uL precipitant. Streak seeding followed by micro-seeding immediately after pipetting with no pre-equilibration of the drop. Controlled hydration experiment for data collection.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.77 α = 90
b = 113.32 β = 90
c = 48.8 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M Be CRL 2016-09-30
Diffraction Radiation
Monochromator Protocol
C110 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 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
1.9 78.85 98.9 0.049 -- -- 3.55 -- 48102 -- -- 33.4
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)
1.9 1.94 95.8 0.868 -- 2.0 3.36 --

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 1.9 78.85 -- -- -- 45558 2460 98.57 -- 0.17905 0.17686 0.219 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 1.902 1.951 -- 171 3225 0.335 0.413 -- 95.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.477
Anisotropic B[1][1] -1.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.69
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_long_range_B_other 9.531
r_scbond_it 4.228
r_scangle_other 6.464
r_angle_other_deg 1.041
r_dihedral_angle_3_deg 16.421
r_mcangle_it 4.615
r_angle_refined_deg 1.611
r_long_range_B_refined 9.543
r_bond_other_d 0.002
r_dihedral_angle_2_deg 36.615
r_bond_refined_d 0.014
r_dihedral_angle_1_deg 5.898
r_chiral_restr 0.099
r_scbond_other 4.212
r_mcangle_other 4.615
r_gen_planes_other 0.002
r_mcbond_it 2.887
r_mcbond_other 2.886
r_dihedral_angle_4_deg 19.434
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4637
Nucleic Acid Atoms 0
Heterogen Atoms 198
Solvent Atoms 242

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0189
AutoPROC data collection
EDNA data collection
XSCALE data scaling
pointless data scaling
BALBES phasing
ARP/wARP model building
XDS data reduction