6KCL | pdb_00006kcl

Crystal structure of Plasmodium falciparum HPPK-DHPS A437G/K540E with pterin and p-hydroxybenzoate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JWR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	9	298	0.1 M bicine buffer pH 9.0, 0.5-0.6 M Ca acetate and 20%w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.323	α = 90
b = 136.44	β = 90
c = 137.699	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2013-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	30	99.9	0.05	0.054	0.022	16.5	6.2		51949

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	2.7	2.8	100		0.364	0.398	0.158	0.955		6.2

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 (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	6JWR	2.7	30	46023	5154	98.36	0.206	0.2018	0.2	0.2434	0.24	RANDOM	50.471

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]
-0.07			-0.47		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.698
r_dihedral_angle_4_deg	18.221
r_dihedral_angle_3_deg	17.853
r_dihedral_angle_1_deg	6.16
r_angle_refined_deg	1.322
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8903
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	130

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

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.