2Q8Z

Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase complexed with 6-amino-UMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q8L	PDB entry 2Q8L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	30% PEG 1000, 100mM Ammonium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.497	α = 90
b = 83.885	β = 90
c = 89.608	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		2007-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

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	1.8	50	94.41	0.097	0.097	10.1	4.9	51328	51328

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	1.8	1.83	97		0.435	0.435	2.7	4.8	2826

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2Q8L	1.8	24.57	51328	51328	2752	94.41	0.16916	0.16916	0.16693	0.21171	RANDOM	22.266

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]
-0.06			0.8		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.903
r_dihedral_angle_4_deg	22.086
r_dihedral_angle_3_deg	14.657
r_dihedral_angle_1_deg	6.269
r_scangle_it	4.058
r_scbond_it	2.736
r_mcangle_it	1.673
r_angle_refined_deg	1.502
r_mcbond_it	1.085
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.903
r_dihedral_angle_4_deg	22.086
r_dihedral_angle_3_deg	14.657
r_dihedral_angle_1_deg	6.269
r_scangle_it	4.058
r_scbond_it	2.736
r_mcangle_it	1.673
r_angle_refined_deg	1.502
r_mcbond_it	1.085
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.292
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.11
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5354
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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 R01GM157729.