1MF4

Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Temperature 295.0
Details sodium phosphate, CaCl2, ethanol; Co-crystallation of protein: peptide in 1:10 molar ratio, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 6.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.78 α = 90
b = 42.78 β = 90
c = 65.87 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 290
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MONOCHROMATOR 2001-06-10
Diffraction Radiation
Monochromator Protocol
GRAPHITE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
1.9 20 93.2 -- 0.073 -- 1.04 -- 8247 -- -3.0 20.63
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)
1.9 1.97 61.3 -- 0.289 1.9 -- --

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 1.9 19.54 -- 0.0 8247 8247 411 100.0 -- 0.184 0.182 0.239 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 1.9 1.95 -- 18 314 0.268 0.27 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.5
Anisotropic B[1][1] -0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.49
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.903
r_scbond_it 2.472
r_mcangle_it 1.769
r_nbd_refined 0.292
r_gen_planes_refined 0.006
r_chiral_restr 0.109
r_dihedral_angle_3_deg 17.004
r_dihedral_angle_2_deg 17.004
r_dihedral_angle_1_deg 3.468
r_angle_refined_deg 1.748
r_bond_refined_d 0.011
r_xyhbond_nbd_refined 0.167
r_symmetry_vdw_refined 0.449
r_symmetry_hbond_refined 0.689
r_mcbond_it 0.88
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 950
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 105

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection