3EZ3 | pdb_00003ez3

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20 % PEG3350 0.2 M Li2SO4 0.1 M Tris 8.5 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.266	α = 90
b = 109.696	β = 90
c = 139.529	γ = 90

Symmetry
Space Group	P 21 21 21

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 270		2007-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9197	CHESS	F1

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	2.304	25	100	0.184	0.127	10.667	7.3	72585	72515			44.9

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	2.304	2.49	99.9		0.689	1.4	7	7173

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.304	24.43	75940	72250	3633	95.13	0.229	0.229	0.226	0.22	0.291	0.28	RANDOM	24.385

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]
-0.01			0.1		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.799
r_dihedral_angle_4_deg	20.629
r_dihedral_angle_3_deg	17.325
r_dihedral_angle_1_deg	6.116
r_scangle_it	2.648
r_scbond_it	1.819
r_angle_refined_deg	1.649
r_mcangle_it	1.105
r_mcbond_it	0.661
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.799
r_dihedral_angle_4_deg	20.629
r_dihedral_angle_3_deg	17.325
r_dihedral_angle_1_deg	6.116
r_scangle_it	2.648
r_scbond_it	1.819
r_angle_refined_deg	1.649
r_mcangle_it	1.105
r_mcbond_it	0.661
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.115
r_symmetry_hbond_refined	0.098
r_metal_ion_refined	0.075
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11546
Nucleic Acid Atoms
Solvent Atoms	561
Heterogen Atoms	158

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.