3SW2

X-ray crystal structure of human FXA in complex with 6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 15-22% w/v PEG5000 MME, 0.01 M calcium acetate, 0.35 M sodium acetate, 0.1 M lithium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.02 α = 90
b = 72.51 β = 90
c = 77.96 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 ADSC QUANTUM 210 -- 2009-06-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-BM -- APS 17-BM

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
2.42 77.96 99.6 0.059 -- -- 5.5 -- 12780 -- 0.0 --
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)
2.42 2.55 97.8 0.381 -- 2.7 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 2.42 32.876 -- 1.36 -- 12724 1126 99.32 -- 0.1992 0.1934 0.2623 --
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 2.4202 2.5303 -- 133 1363 0.2984 0.4004 -- 97.0
X Ray Diffraction 2.5303 2.6636 -- 138 1425 0.2689 0.4053 -- 100.0
X Ray Diffraction 2.6636 2.8304 -- 140 1435 0.2358 0.3276 -- 100.0
X Ray Diffraction 2.8304 3.0488 -- 141 1440 0.224 0.3335 -- 100.0
X Ray Diffraction 3.0488 3.3554 -- 141 1467 0.1825 0.2855 -- 100.0
X Ray Diffraction 3.3554 3.8403 -- 140 1451 0.176 0.237 -- 100.0
X Ray Diffraction 3.8403 4.8359 -- 145 1480 0.1601 0.2173 -- 99.0
X Ray Diffraction 4.8359 32.8786 -- 148 1537 0.1941 0.2302 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 16.829
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.768
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 22.1384
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.072
f_bond_d 0.009
f_angle_d 1.085
f_dihedral_angle_d 14.635
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2134
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 83

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
AMoRE phasing
PHENIX refinement version: (PHENIX.REFINE: DEV_501)
XDS data reduction
SCALA data scaling