2W41

Crystal structure of Plasmodium falciparum glycerol kinase with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BU6	PDB ENTRY 1BU6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		50MM KFORMATE, 20% PEG 3350, 25% ETHYLENE GLYCOL, 10MM LDAO, 20MM GLYCEROL, THEN SOAKED WITH 5 MM ADP AND 10 MM MGCL2, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.529	α = 90
b = 57.632	β = 89.75
c = 123.922	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	CCD	ADSC CCD		2006-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.41	124.03	91.4	0.1	10.95	3.7		39660		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	2.41	2.47	40.5		0.84	0.71	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BU6	2.41	124.03	39660	2120	91.3	0.2	0.197	0.258	RANDOM	43.23

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]
-0.28		-0.05	-1.22		1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.374
r_dihedral_angle_3_deg	17.968
r_dihedral_angle_4_deg	17.11
r_dihedral_angle_1_deg	7.405
r_scangle_it	3.599
r_scbond_it	2.317
r_angle_refined_deg	1.77
r_mcangle_it	1.433
r_mcbond_it	0.839
r_nbtor_refined	0.305
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.193
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8032
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing