1Z1Y | pdb_00001z1y

Crystal structure of Methylated Pvs25, an ookinete protein from Plasmodium vivax

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	PEG1500, sodium accetate, ammonium accetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.9	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.164	α = 90
b = 43.7	β = 103.15
c = 65.65	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 QUANTUM 4		2004-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.09524	APS	22-ID

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	28.6	98.7	0.083	0.083	12.4	7.4	21617	21346		-3	14.7

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)
	2	2.1	98.1		0.187	0.187	5.2		21346

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	SAD	THROUGHOUT	2	28.6	21346	20249	1095	98.75	0.245	0.245	0.244	0.2394	0.276	0.2453	RANDOM	31.98

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]
1.03		0.56	-0.42		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.071
r_dihedral_angle_3_deg	15.481
r_dihedral_angle_1_deg	6.038
r_scangle_it	3.069
r_scbond_it	1.826
r_angle_refined_deg	1.364
r_mcangle_it	1.203
r_mcbond_it	0.751
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.071
r_dihedral_angle_3_deg	15.481
r_dihedral_angle_1_deg	6.038
r_scangle_it	3.069
r_scbond_it	1.826
r_angle_refined_deg	1.364
r_mcangle_it	1.203
r_mcbond_it	0.751
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.305
r_nbd_refined	0.226
r_symmetry_metal_ion_refined	0.188
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.148
r_metal_ion_refined	0.121
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2732
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	9

Software

Software
Software Name	Purpose
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
XDS	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.