5PZP

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 4-FLUORO-2-(4-FLUOROPHENYL)-N-METHYL-5-(2-METHYL-5-{[1-(PYRIMIDIN-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-BENZOFURAN-3-CARBOXAMIDE (BMS-929075)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 277.0
Details 100 mM sodium citrate, pH 5.6, 1.75 M (NH4)2SO4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.2 α = 90
b = 90.7 β = 90
c = 234.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2009-09-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-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
2.95 50 99.8 -- 0.088 -- 3.6 -- 30164 -- 0.0 74.45
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)
2.95 3.06 99.9 -- 0.478 2.7 3.7 --

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 2.95 43.86 -- 0.0 -- 30104 1057 99.7 -- 0.201 0.199 0.244 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 2.95 3.05 -- 102 2753 0.225 0.306 -- 98.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 66.79
Anisotropic B[1][1] -15.0753
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.658
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 18.7333
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 17.53
t_bond_d 0.01
t_omega_torsion 2.85
t_angle_deg 1.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8285
Nucleic Acid Atoms 0
Heterogen Atoms 238
Solvent Atoms 10

Software

Software
Software Name Purpose
HKL-2000 data collection
HKL-2000 data scaling
AMoRE phasing
BUSTER refinement version: 2.11.7
PDB_EXTRACT data extraction version: 3.22
HKL-2000 data reduction