2QU8

Crystal structure of putative nucleolar GTP-binding protein 1 PFF0625w from Plasmodium falciparum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	28% PEG 2000 MME, 0.1 M Bis-Tris pH 6.5, 1 mM GDP, 2 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2	VAPOR DIFFUSION, HANGING DROP	5.2	298	28% PEG 3350, 0.2 M NaCl, 0.1 M Na Cacodylate pH 5.2, 1 mM GDP, 2 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.377	α = 90
b = 77.162	β = 90
c = 40.196	γ = 90

Symmetry
Space Group	P 21 21 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 315		2007-06-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2007-05-03	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97937	APS	19-ID
2	ROTATING ANODE	RIGAKU FR-E+ DW	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.01	50	100	0.076	0.041	11.9	6.9	12175	12175

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.01	2.08	100		0.441	0.301	3.25	6.5	1181

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	SAD	THROUGHOUT	2.01	32.72	12151	12139	580	99.99	0.225	0.225	0.223	0.264	RANDOM	37.034

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			-0.58		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.189
r_dihedral_angle_4_deg	27.388
r_dihedral_angle_3_deg	15.968
r_dihedral_angle_1_deg	5.64
r_scangle_it	1.803
r_angle_refined_deg	1.187
r_scbond_it	1.122
r_mcangle_it	1.025
r_mcbond_it	0.578
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.189
r_dihedral_angle_4_deg	27.388
r_dihedral_angle_3_deg	15.968
r_dihedral_angle_1_deg	5.64
r_scangle_it	1.803
r_angle_refined_deg	1.187
r_scbond_it	1.122
r_mcangle_it	1.025
r_mcbond_it	0.578
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.122
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	28

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SHELXD	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 R01GM133198.