8D1P

Crystal structure of Plasmodium falciparum GRP78-NBD in complex with 7-Deaza-2'-C-methyladenosine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62980.7 M (NH4)2SO4, 1.2 M Li2SO4, 0.1 M NaCitrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.5765.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.265α = 90
b = 84.265β = 90
c = 291.778γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

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
11.885099.90.05635.218.951027
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.885.610.43

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 REPLACEMENTTHROUGHOUT5UMB1.8845.6248462256499.930.188850.187380.21638RANDOM30.408
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]
0.760.380.76-2.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.299
r_dihedral_angle_4_deg24.385
r_dihedral_angle_3_deg15.167
r_long_range_B_refined8.133
r_long_range_B_other8.116
r_scangle_other7.063
r_dihedral_angle_1_deg6.097
r_scbond_other4.717
r_scbond_it4.715
r_mcangle_it3.628
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.299
r_dihedral_angle_4_deg24.385
r_dihedral_angle_3_deg15.167
r_long_range_B_refined8.133
r_long_range_B_other8.116
r_scangle_other7.063
r_dihedral_angle_1_deg6.097
r_scbond_other4.717
r_scbond_it4.715
r_mcangle_it3.628
r_mcangle_other3.62
r_mcbond_it2.949
r_mcbond_other2.948
r_angle_refined_deg1.781
r_angle_other_deg1.458
r_chiral_restr0.092
r_bond_refined_d0.013
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 Atoms278
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing