4ADT

Crystal structure of plasmodial PLP synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NV2PDB ENTRY 2NV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4249.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.471α = 90
b = 180.471β = 90
c = 102.042γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.425099.90.0821.66.72437046.5
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)
12.422.4698.40.463.14.5

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 2NV22.425023093124299.880.185070.182630.23236RANDOM44.379
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]
-0.19-0.09-0.190.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_3_deg17.532
r_dihedral_angle_4_deg16.983
r_dihedral_angle_1_deg6.699
r_scangle_it4.338
r_scbond_it2.632
r_angle_refined_deg1.678
r_mcangle_it1.674
r_angle_other_deg1.164
r_mcbond_it0.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_3_deg17.532
r_dihedral_angle_4_deg16.983
r_dihedral_angle_1_deg6.699
r_scangle_it4.338
r_scbond_it2.632
r_angle_refined_deg1.678
r_mcangle_it1.674
r_angle_other_deg1.164
r_mcbond_it0.878
r_mcbond_other0.139
r_chiral_restr0.093
r_bond_refined_d0.018
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
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 Atoms4062
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing