7ZCZ

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 1-(4-chlorophenyl)methanamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293200mM NaCl, 15%(w/v)PEG3350, 100mM bis-tris propane, 2%(v/v)DMSO
Crystal Properties
Matthews coefficientSolvent content
2.9958.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.659α = 90
b = 103.628β = 117.455
c = 86.864γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291PIXELDECTRIS PILATUS 6M2017-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.033200PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.4545.0499.10.0450.0620.0430.99912.23.449863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.530.5210.7120.4820.7973.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5ILQ2.4543.42549842238499.1130.1780.17570.217760.676
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]
-2.0220.6233.461-1.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.735
r_dihedral_angle_4_deg17.337
r_dihedral_angle_3_deg16.956
r_dihedral_angle_1_deg7.506
r_lrange_it6.894
r_lrange_other6.875
r_scangle_it4.652
r_scangle_other4.613
r_mcangle_it4.386
r_mcangle_other4.386
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.735
r_dihedral_angle_4_deg17.337
r_dihedral_angle_3_deg16.956
r_dihedral_angle_1_deg7.506
r_lrange_it6.894
r_lrange_other6.875
r_scangle_it4.652
r_scangle_other4.613
r_mcangle_it4.386
r_mcangle_other4.386
r_scbond_it3.144
r_scbond_other3.023
r_mcbond_it2.821
r_mcbond_other2.821
r_angle_refined_deg1.83
r_angle_other_deg1.336
r_nbd_other0.285
r_nbd_refined0.221
r_symmetry_nbd_refined0.216
r_symmetry_nbd_other0.196
r_xyhbond_nbd_refined0.195
r_nbtor_refined0.172
r_symmetry_xyhbond_nbd_refined0.154
r_ncsr_local_group_30.102
r_ncsr_local_group_10.098
r_ncsr_local_group_20.088
r_chiral_restr0.086
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_other0.075
r_metal_ion_refined0.063
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8161
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing