1TG1 | pdb_00001tg1

Crystal Structure of the complex formed between russells viper phospholipase A2 and a designed peptide inhibitor PHQ-Leu-Val-Arg-Tyr at 1.2A 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, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4848.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.496α = 90
b = 52.496β = 90
c = 47.93γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARRESEARCHmirror2004-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.981EMBL/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
11.2301000.07720.15.83517410.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2799.40.4542.2

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 (All)R-Factor (Observed)R-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1skg1.2529.3635174351749211000.18840.18840.188160.1971RANDOM12.325
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]
0.090.09-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.731
r_dihedral_angle_1_deg6.902
r_scangle_it2.243
r_angle_refined_deg2.026
r_scbond_it1.454
r_mcangle_it1.2
r_angle_other_deg1.046
r_mcbond_it0.648
r_nbd_refined0.434
r_nbd_other0.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.731
r_dihedral_angle_1_deg6.902
r_scangle_it2.243
r_angle_refined_deg2.026
r_scbond_it1.454
r_mcangle_it1.2
r_angle_other_deg1.046
r_mcbond_it0.648
r_nbd_refined0.434
r_nbd_other0.245
r_symmetry_vdw_other0.237
r_symmetry_vdw_refined0.235
r_symmetry_hbond_refined0.217
r_xyhbond_nbd_refined0.195
r_xyhbond_nbd_other0.119
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms982
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing