1SV9

Crystal structure of the complex formed between groupII phospholipase A2 and anti-inflammatory agent 2-[(2,6-Dichlorophenyl)amino] benzeneacetic acid at 2.7A resolution


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 297.0
Details 0.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.05 α = 90
b = 53.05 β = 90
c = 48.43 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRROR 2004-03-20
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.7 20 90.0 -- 0.119 -- 12.41 3463 3463 0.0 0.0 36.4
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)
2.7 2.76 75.0 -- 0.206 2.1 -- --

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 2.71 18.76 -- 0.0 3463 3463 175 87.8 0.198 0.196 0.196 0.238 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 2.7 2.87 303 13 303 0.282 0.298 0.083 51.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.0
Anisotropic B[1][1] 2.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.76
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 2.61
c_mcbond_it 1.53
c_improper_angle_d 0.8
c_scbond_it 2.25
c_bond_d 0.008
c_dihedral_angle_d 22.5
c_angle_deg 1.5
c_scangle_it 3.38
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.31
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.29
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 944
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 53

Software

Software
Software Name Purpose
CNS refinement version: 0.9
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing