2B94

Structural analysis of P knowlesi homolog of P falciparum PNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SQ6pdb entries 1SQ6, 1NW4
experimental modelPDB 1NW4pdb entries 1SQ6, 1NW4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293sodium thiosulfate, MOPS, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.377α = 90
b = 98.377β = 90
c = 160.08γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.9184ALS8.2.1

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
11.8541.169396.90.87137.42491624916-324.193
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)
11.851.9581.40.7811.94.6

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 REPLACEMENTTHROUGHOUTpdb entries 1SQ6, 1NW41.8514.992359123591125796.850.188590.188590.186740.22498RANDOM27.461
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.632
r_dihedral_angle_4_deg13.175
r_dihedral_angle_3_deg11.334
r_dihedral_angle_1_deg5.359
r_scangle_it4.137
r_scbond_it3.21
r_mcangle_it2.826
r_mcbond_it2.045
r_angle_refined_deg1.152
r_angle_other_deg0.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.632
r_dihedral_angle_4_deg13.175
r_dihedral_angle_3_deg11.334
r_dihedral_angle_1_deg5.359
r_scangle_it4.137
r_scbond_it3.21
r_mcangle_it2.826
r_mcbond_it2.045
r_angle_refined_deg1.152
r_angle_other_deg0.751
r_mcbond_other0.473
r_symmetry_vdw_other0.263
r_nbd_refined0.195
r_symmetry_vdw_refined0.194
r_nbd_other0.171
r_nbtor_refined0.167
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.14
r_nbtor_other0.08
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1807
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing