7ZEA | pdb_00007zea

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor O-benzylhydroxylamine

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
2.91	57.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.025	α = 90
b = 104.507	β = 117.47
c = 87.301	γ = 90

Symmetry
Space Group	P 1 21 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		2017-12-03	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	2.448	45.278	99.4	0.051	0.07	0.048	0.999	11.3	3.4		50829

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	2.45	2.52			0.464	0.643	0.443	0.852		3.3

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	2.448	45.278	50809	2430	99.306	0.184	0.1821	0.19	0.2231	0.22	53.665

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]
-1.472		0.097	4.451		-1.999

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.333
r_dihedral_angle_4_deg	19.132
r_dihedral_angle_3_deg	16.603
r_dihedral_angle_1_deg	7.037
r_lrange_it	6.423
r_lrange_other	6.383
r_scangle_it	4.292
r_scangle_other	4.273
r_mcangle_it	3.949
r_mcangle_other	3.949
r_scbond_it	2.755
r_scbond_other	2.713
r_mcbond_it	2.516
r_mcbond_other	2.514
r_angle_refined_deg	1.87
r_angle_other_deg	1.347
r_symmetry_nbd_refined	0.486
r_nbd_other	0.443
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_xyhbond_nbd_other	0.116
r_ncsr_local_group_3	0.105
r_metal_ion_refined	0.099
r_ncsr_local_group_1	0.095
r_chiral_restr	0.089
r_ncsr_local_group_2	0.086
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8117
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	29

Software

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