6HL7 | pdb_00006hl7

Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with mutated active site (R109A/K138A) and N-carbamoyl-L-phosphate bound

X-RAY DIFFRACTION

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		293	0.2M Potassium citrate tribasic monohydrate 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.001	α = 90
b = 89.715	β = 122.17
c = 121.642	γ = 90

Symmetry
Space Group	C 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	100	PIXEL	DECTRIS PILATUS 6M		2016-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	57.61	97.6	0.066	0.999	12.95	3.16		46404		1.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	94		0.957	0.619		3.21

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5ilq	2.5	57.61	43356	2399	98.01	0.207	0.2042	0.21	0.2578	0.26	RANDOM	65.452

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]
-0.15		-0.02	0.13		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.932
r_dihedral_angle_3_deg	20.426
r_dihedral_angle_4_deg	18.786
r_dihedral_angle_1_deg	9.004
r_mcangle_it	5.477
r_mcbond_it	3.421
r_mcbond_other	3.42
r_angle_other_deg	2.412
r_angle_refined_deg	1.946
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.932
r_dihedral_angle_3_deg	20.426
r_dihedral_angle_4_deg	18.786
r_dihedral_angle_1_deg	9.004
r_mcangle_it	5.477
r_mcbond_it	3.421
r_mcbond_other	3.42
r_angle_other_deg	2.412
r_angle_refined_deg	1.946
r_chiral_restr	0.088
r_bond_other_d	0.035
r_bond_refined_d	0.01
r_gen_planes_other	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7870
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
EDNA	data collection
DIMPLE	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.