1YJ8

Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10	293	PEG 400, Potassium phosphate monobasic, CAPS, DTT, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.3	71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.455	α = 90
b = 177.455	β = 90
c = 232.699	γ = 120

Symmetry
Space Group	P 63 2 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	ADSC QUANTUM 210		2004-06-11	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 210		2004-06-20	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-3		SSRL	BL11-3
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794, 0.91840, 0.97950	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.85	50	99.3	0.132	8.4	5.3	50738	50574		-3	69.775

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.85	3	96.3		0.708	1.8	4.3	7016

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.85	44.54	47958	47958	2557	99.05	0.23706	0.23706	0.23607	0.25576	RANDOM	56.225

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.426
r_dihedral_angle_3_deg	14.926
r_dihedral_angle_4_deg	14.453
r_dihedral_angle_1_deg	4.761
r_scangle_it	2.229
r_mcangle_it	1.694
r_scbond_it	1.406
r_mcbond_it	1.011
r_angle_refined_deg	0.944
r_angle_other_deg	0.73
r_symmetry_vdw_other	0.221
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.188
r_nbtor_refined	0.171
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.127
r_mcbond_other	0.113
r_symmetry_hbond_refined	0.09
r_nbtor_other	0.081
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8415
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing