X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Details SOAKING WITH COMPOUND MK3281 WAS PERFORMED AT 4 DEG C BY TRANSFERRING THE APO-NS5B CRYSTALS FOR 10 MIN IN A SOLUTION CONTAINING 100 MM 2-MORPHOLINOETHANESULFONIC ACID (MES), PH 6.0, 14% POLYETHYLENE GLYCOL (PEG) 8,000, 14% 2- PROPANOL, 2.5 MM TCEP, 10 MM MNCL2 AND 2.5 MM OF COMPOUND MK3281. THE CRYSTALS WERE THEN TRANSFERRED FOR 1 MIN TO A CRYO-PROTECTANT SOLUTION CONTAINING 100 MM MES PH 6.0, 14% POLYETHYLENE GLYCOL PEG 8,000, 14% 2-PROPANOL, 18% 2-METHYL-2,5 PENTANEDIOL (MPD), 2.5 MM TCEP, 5 MM MNCL2 AND 1.25 MM COMPOUND MK3281 AND THEN PLUNGED DIRECTLY INTO LIQUID NITROGEN.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.98 α = 90
b = 94.27 β = 90
c = 95.14 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
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
2.53 20 99.7 0.09 -- -- 3.9 -- 20692 -- 1.0 --
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)
2.53 2.67 99.7 0.53 -- 1.5 3.8 --

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 2.53 95.35 -- -- -- 19605 1056 99.63 -- 0.23727 0.23332 0.31016 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 2.53 2.596 -- 70 1384 0.346 0.412 -- 97.39
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.851
Anisotropic B[1][1] 1.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.17
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 0.916
r_dihedral_angle_3_deg 18.535
r_dihedral_angle_4_deg 17.26
r_dihedral_angle_2_deg 33.962
r_scbond_it 1.543
r_bond_refined_d 0.012
r_scangle_it 2.504
r_angle_refined_deg 1.349
r_dihedral_angle_1_deg 5.734
r_mcbond_it 0.468
r_chiral_restr 0.085
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3911
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 130

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0102
MOSFLM data reduction
SCALA data scaling
AMoRE phasing