8D1Y

Crystal structure of Plasmodium falciparum GRP78 in complex with Trans-Zeatin Riboside


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
3.3363.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.876α = 90
b = 83.876β = 90
c = 291.225γ = 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)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
11.9501000.0826.4418.549029
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)
11.95.660.51

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 REPLACEMENTTHROUGHOUT5UMB1.948.5846588243999.990.193390.191910.22162RANDOM25.353
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]
0.650.330.65-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg17.827
r_dihedral_angle_3_deg14.75
r_long_range_B_refined7.247
r_long_range_B_other7.174
r_dihedral_angle_1_deg6.14
r_scangle_other6.116
r_scbond_other4.099
r_scbond_it4.098
r_mcangle_it3.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg17.827
r_dihedral_angle_3_deg14.75
r_long_range_B_refined7.247
r_long_range_B_other7.174
r_dihedral_angle_1_deg6.14
r_scangle_other6.116
r_scbond_other4.099
r_scbond_it4.098
r_mcangle_it3.13
r_mcangle_other3.129
r_mcbond_it2.483
r_mcbond_other2.481
r_angle_refined_deg1.816
r_angle_other_deg1.471
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms311
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing