2FFC

Crystal Structure of Plasmodium Vivax Orotidine-Monophosphate-Decarboxyl UMP Bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AQW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.529630.0% PEG 4K, 0.2M NaOAc, 0.1M Tris HCl, VAPOR DIFFUSION, pH 8.5, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.141.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.817α = 90
b = 69.588β = 90
c = 59.338γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3Si 1112005-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1.0APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.75097.70.0520.05210.26.8371093710929.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7280.30.6120.6121.64.71473

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2AQW1.750361273612794497.680.188250.188250.187030.23444RANDOM25.437
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]
-0.930.220.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.829
r_dihedral_angle_4_deg18.714
r_dihedral_angle_3_deg14.237
r_dihedral_angle_1_deg5.747
r_scangle_it4.199
r_scbond_it2.746
r_mcangle_it1.719
r_angle_refined_deg1.585
r_mcbond_it1.179
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.829
r_dihedral_angle_4_deg18.714
r_dihedral_angle_3_deg14.237
r_dihedral_angle_1_deg5.747
r_scangle_it4.199
r_scbond_it2.746
r_mcangle_it1.719
r_angle_refined_deg1.585
r_mcbond_it1.179
r_nbtor_refined0.31
r_nbd_refined0.21
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.146
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2570
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building