2AQW

Structure of putative orotidine-monophosphate-decarboxylase from Plasmodium yoelii (PY01515)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	297	2.5 M (NH4)2SO4, Bis-Tris propane pH 7.0 and 10mM NaI, VAPOR DIFFUSION, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.632	α = 90
b = 61.632	β = 90
c = 274.284	γ = 120

Symmetry
Space Group	P 61 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 4	Si111	2005-07-23	M	MAD
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	VeriMax	2005-08-11	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.9797	APS	17-ID
2	ROTATING ANODE	RIGAKU FR-E	1.54

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	20	99.1	0.9	0.9	9.1	6	21954	21895			28.6

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	2.07	97.1		0.546	0.546	2.35	4.8	2073

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	20	21954	21145	710	99.27	0.21217	0.21217	0.21057	0.26154	RANDOM	29.695

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]
1.53	0.77		1.53		-2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.264
r_dihedral_angle_4_deg	22
r_dihedral_angle_3_deg	16.224
r_dihedral_angle_1_deg	6.316
r_scangle_it	3.837
r_scbond_it	2.736
r_mcangle_it	1.678
r_angle_refined_deg	1.673
r_mcbond_it	1.086
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.271
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.18
r_symmetry_vdw_refined	0.174
r_chiral_restr	0.129
r_bond_refined_d	0.023
r_gen_planes_refined	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2633
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
SOLVE	phasing
O	model building