5JMW | pdb_00005jmw

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JAZ	5JAZ (LC51)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	12.5% W/V PEG 1000, 12.5% PEG 3350, 12.5% v/v MPD 0.03M of each ethylene glycol 0.1M MOPS/HEPES-Na pH 7.5 (0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol)

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.43	α = 103.57
b = 56.193	β = 103.07
c = 86.046	γ = 100.4

Symmetry
Space Group	P 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 PILATUS3 6M		2015-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979490	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	28.96	96.4	0.071	0.998	10.2	3.6		123676			13

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	1.55	1.58	87.9		0.49	1.7	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 (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	5JAZ (LC51)	1.55	28	117573	6099	96.35	0.18143	0.18036	0.19	0.20204	0.21	RANDOM	18.657

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]
-0.19	0.2	-0.8	1.02	-0.42	-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.113
r_dihedral_angle_4_deg	21.001
r_dihedral_angle_3_deg	12.547
r_dihedral_angle_1_deg	5.547
r_long_range_B_refined	3.828
r_long_range_B_other	3.626
r_scangle_other	1.71
r_mcangle_it	1.494
r_mcangle_other	1.494
r_angle_refined_deg	1.176
r_scbond_it	1.017
r_scbond_other	1.017
r_angle_other_deg	0.867
r_mcbond_it	0.849
r_mcbond_other	0.849
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6552
Nucleic Acid Atoms
Solvent Atoms	545
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
O	model building