4CKU

Three dimensional structure of plasmepsin II in complex with hydroxyethylamine-based inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.50.1M CITRIC ACID, PH 4.5, 0.3M AMMONIUM ACETATE, 25% PEG 3350, PROTEIN 10 MG/ML, VAPOR DIFFUSION, SITTING DROP, TIME 2-4 WEEKS.
Crystal Properties
Matthews coefficientSolvent content
2.2946.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 201.95α = 90
b = 115.25β = 110.75
c = 93.17γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2011-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-3MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8530980.079.22.616609916.852
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9599.40.283.52.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BJU1.8529.98157768832597.870.16040.157830.2089RANDOM24.732
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]
0.01-0.02-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.071
r_dihedral_angle_4_deg17.45
r_dihedral_angle_3_deg14.193
r_dihedral_angle_1_deg7.105
r_mcangle_it3.589
r_scbond_it3.282
r_mcbond_it2.394
r_mcbond_other2.389
r_angle_refined_deg1.866
r_angle_other_deg0.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.071
r_dihedral_angle_4_deg17.45
r_dihedral_angle_3_deg14.193
r_dihedral_angle_1_deg7.105
r_mcangle_it3.589
r_scbond_it3.282
r_mcbond_it2.394
r_mcbond_other2.389
r_angle_refined_deg1.866
r_angle_other_deg0.877
r_chiral_restr0.121
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15308
Nucleic Acid Atoms
Solvent Atoms1189
Heterogen Atoms294

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling