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 (QUANTUM 210) ADSC -- --
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_scangle_it 2.504
r_scbond_it 1.543
r_mcangle_it 0.916
r_mcbond_it 0.468
r_gen_planes_refined 0.006
r_chiral_restr 0.085
r_dihedral_angle_4_deg 17.26
r_dihedral_angle_3_deg 18.535
r_dihedral_angle_2_deg 33.962
r_dihedral_angle_1_deg 5.734
r_angle_refined_deg 1.349
r_bond_refined_d 0.012
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0102 refinement
AMORE model building