8D20

Crystal structure of Plasmodium falciparum GRP78 in complex with 5'-Methylthioadenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UMB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.7 M (NH4)2SO4, 1.2 M Li2SO4, 0.1 M NaCitrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.3763.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.322α = 90
b = 84.322β = 90
c = 291.748γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2021-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.5212CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.955097.30.080.5237.9619.244948
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.060.510.52

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 REPLACEMENTTHROUGHOUT5UMB1.9545.6342772217297.270.195520.193910.22687RANDOM23.308
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]
0.660.330.66-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_dihedral_angle_4_deg22.21
r_dihedral_angle_3_deg14.956
r_long_range_B_refined6.593
r_long_range_B_other6.558
r_dihedral_angle_1_deg6.231
r_scangle_other5.464
r_scbond_it3.604
r_scbond_other3.594
r_mcangle_it2.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_dihedral_angle_4_deg22.21
r_dihedral_angle_3_deg14.956
r_long_range_B_refined6.593
r_long_range_B_other6.558
r_dihedral_angle_1_deg6.231
r_scangle_other5.464
r_scbond_it3.604
r_scbond_other3.594
r_mcangle_it2.925
r_mcangle_other2.925
r_mcbond_it2.315
r_mcbond_other2.314
r_angle_refined_deg1.8
r_angle_other_deg1.466
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2951
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing