1TH6 | pdb_00001th6

Crystal structure of phospholipase A2 in complex with atropine at 1.23A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SKGpdb entry 1SKG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72980.2M ammonium sulphate, 30% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.447.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.331α = 90
b = 52.331β = 90
c = 48.071γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARRESEARCHMirror2004-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.803EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2351.9999.820.05333.23750437504
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.231.251003.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1SKG1.2351.99375043666776799.820.189090.188770.20444RANDOM14.146
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.190.19-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.451
r_dihedral_angle_1_deg3.975
r_scangle_it2.164
r_angle_refined_deg1.946
r_scbond_it1.399
r_mcangle_it1.191
r_angle_other_deg0.79
r_mcbond_it0.635
r_nbd_refined0.435
r_symmetry_hbond_refined0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.451
r_dihedral_angle_1_deg3.975
r_scangle_it2.164
r_angle_refined_deg1.946
r_scbond_it1.399
r_mcangle_it1.191
r_angle_other_deg0.79
r_mcbond_it0.635
r_nbd_refined0.435
r_symmetry_hbond_refined0.235
r_nbd_other0.213
r_chiral_restr0.211
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_refined0.2
r_symmetry_vdw_other0.162
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms943
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing