4KP7 | pdb_00004kp7

Structure of Plasmodium IspC in complex with a beta-thia-isostere derivative of Fosmidomycin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AU8	3AU8; IspC Plasmodium Apo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	2% PEG4000, 100 mM NaAc, 15% MPD, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.46	α = 90
b = 78.12	β = 91.53
c = 99.99	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	100	PIXEL	PSI PILATUS 6M		2011-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2	40	97.1	0.082	12.7	3.8	53593	52039	2	2

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	2	2.1	96.7		0.533	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3AU8; IspC Plasmodium Apo	2	15	49419	49419	2601	97.06	0.195	0.18806	0.18485	0.18	0.24871	0.25	RANDOM	36.982

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]
-2.41		-0.09	4.26		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.417
r_sphericity_free	31.56
r_sphericity_bonded	19.793
r_dihedral_angle_3_deg	17.925
r_dihedral_angle_4_deg	10.827
r_dihedral_angle_1_deg	4.816
r_rigid_bond_restr	4.551
r_angle_refined_deg	1.2
r_chiral_restr	0.08
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.417
r_sphericity_free	31.56
r_sphericity_bonded	19.793
r_dihedral_angle_3_deg	17.925
r_dihedral_angle_4_deg	10.827
r_dihedral_angle_1_deg	4.816
r_rigid_bond_restr	4.551
r_angle_refined_deg	1.2
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6468
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	86

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.