7ZST | pdb_00007zst

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with FLA-01

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ILQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	200mM NaCl, 15%(w/v)PEG3350, 100mM bis-tris propane, 2%(v/v)DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.284	α = 90
b = 89.735	β = 109.215
c = 137.052	γ = 90

Symmetry
Space Group	I 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	291	PIXEL	DECTRIS PILATUS 6M		2020-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033200	PETRA III, DESY	P11

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	49.504	99.9	0.032	0.045	0.032	0.999	13.3	2		47374

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)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59			0.012	0.016	0.012	0.878		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5ILQ	2.5	49.504	47372	2448	99.93	0.238	0.2359	0.24	0.2824	0.28	57.712

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]
2.637		-4.35	0.688		-0.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.049
r_dihedral_angle_4_deg	21.825
r_dihedral_angle_3_deg	17.952
r_dihedral_angle_1_deg	7.736
r_lrange_it	4.056
r_lrange_other	4.014
r_mcangle_it	2.062
r_mcangle_other	2.062
r_angle_refined_deg	1.671
r_scangle_it	1.631
r_scangle_other	1.605
r_angle_other_deg	1.225
r_mcbond_it	1.193
r_mcbond_other	1.193
r_scbond_it	0.973
r_scbond_other	0.938
r_symmetry_xyhbond_nbd_refined	0.379
r_nbd_other	0.264
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.194
r_symmetry_xyhbond_nbd_other	0.189
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.166
r_metal_ion_refined	0.157
r_ncsr_local_group_2	0.114
r_ncsr_local_group_3	0.109
r_ncsr_local_group_1	0.099
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.075
r_dihedral_angle_other_2_deg	0.024
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7749
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing