4ADU

Crystal structure of plasmodial PLP synthase with bound R5P intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NV1PDB ENTRY 2NV1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M BICINE PH 8.5, 1.6 M LICL
Crystal Properties
Matthews coefficientSolvent content
2.454

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-ray100CCDADSC CCD2010-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.445099.80.0714.66.122508
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)
12.442.4897.80.442.35.4

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 2NV12.445022508121299.810.196290.193350.25RANDOM39.485
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]
-1.54-0.77-1.542.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.92
r_dihedral_angle_3_deg16.772
r_dihedral_angle_4_deg10.959
r_dihedral_angle_1_deg6.157
r_scangle_it3.308
r_scbond_it1.936
r_angle_refined_deg1.461
r_mcangle_it1.28
r_angle_other_deg1.118
r_mcbond_it0.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.92
r_dihedral_angle_3_deg16.772
r_dihedral_angle_4_deg10.959
r_dihedral_angle_1_deg6.157
r_scangle_it3.308
r_scbond_it1.936
r_angle_refined_deg1.461
r_mcangle_it1.28
r_angle_other_deg1.118
r_mcbond_it0.668
r_mcbond_other0.095
r_chiral_restr0.08
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
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_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 Atoms4213
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing