3LZE | pdb_00003lze

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37C catalytic residue mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LX3	3lx3 with mutation and without ligand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	298	2 ul 17 mg/ml protein (in SGPP buffer) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 1 mM TCEP; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 mM NaCl, 20% glycerol, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.495	α = 90
b = 131.495	β = 90
c = 73.67	γ = 120

Symmetry
Space Group	H 3 2

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	MARMOSAIC 325 mm CCD		2009-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	30	99.9	0.077	14.5	9.2		19289		5	43

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	100		0.661	2.5	9.4	1896

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	FOURIER SYNTHESIS	THROUGHOUT	3lx3 with mutation and without ligand	1.9	29.03	19289	1005	99.85	0.193	0.191	0.1961	0.22	0.2246	RANDOM	49.531

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]
-1.81	-0.9		-1.81		2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.703
r_dihedral_angle_4_deg	22.421
r_dihedral_angle_3_deg	14.5
r_scangle_it	6.613
r_dihedral_angle_1_deg	6.417
r_scbond_it	4.7
r_mcangle_it	4.025
r_mcbond_it	2.775
r_angle_refined_deg	1.542
r_mcbond_other	0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.703
r_dihedral_angle_4_deg	22.421
r_dihedral_angle_3_deg	14.5
r_scangle_it	6.613
r_dihedral_angle_1_deg	6.417
r_scbond_it	4.7
r_mcangle_it	4.025
r_mcbond_it	2.775
r_angle_refined_deg	1.542
r_mcbond_other	0.96
r_angle_other_deg	0.862
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1374
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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.