3Q77

Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 293.0
Details 20% w/v PEG3350, 0.2 M ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.73 α = 90
b = 73.73 β = 90
c = 70.66 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2004-08-20
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 -- EMBL/DESY, HAMBURG X31

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 24.13 97.2 0.09 -- -- 11.0 14498 14498 -- -- --
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)
2.0 2.07 79.7 0.35 -- 2.8 10.8 --

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 1.998 24.134 -- 1.36 14498 14457 735 97.16 -- 0.1608 0.1586 0.2032 --
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 1.9976 2.1517 -- 136 2403 0.1963 0.2587 -- 86.0
X Ray Diffraction 2.1517 2.3681 -- 158 2798 0.1702 0.2275 -- 100.0
X Ray Diffraction 2.3681 2.7103 -- 158 2806 0.1565 0.2234 -- 100.0
X Ray Diffraction 2.7103 3.4132 -- 130 2844 0.1544 0.1918 -- 100.0
X Ray Diffraction 3.4132 24.1362 -- 153 2871 0.1484 0.1756 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.4269
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4269
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.8538
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.883
f_plane_restr 0.004
f_bond_d 0.008
f_angle_d 1.152
f_chiral_restr 0.074
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1636
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 136

Software

Software
Software Name Purpose
PHENIX refinement version: 1.6.4_486
AMoRE phasing
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
MAR345dtb data collection