3BAR | pdb_00003bar

Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-azido-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	9.2	293	100mM Ammonium phosphate, 27% PEG 1000, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.928	α = 90
b = 83.354	β = 90
c = 89.872	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	MARMOSAIC 225 mm CCD	DCM with cryo-cooled 1st crystal sagitally bent 2nd crystal followed by vertically focusing mirror	2007-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-1

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	1.9	50	95.37	0.085	0.085	11.4	5.2	44155	44155

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	1.9	1.97	97.9		0.459	0.459	3.45	5.1	4703

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2Q8L	1.9	24.68	44155	44155	2357	95.37	0.17445	0.17445	0.17202	0.17	0.2193	0.22	RANDOM	22.075

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]
0.49			-0.19		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.745
r_dihedral_angle_4_deg	24.013
r_dihedral_angle_3_deg	14.035
r_dihedral_angle_1_deg	5.871
r_scangle_it	3.725
r_scbond_it	2.53
r_mcangle_it	1.613
r_angle_refined_deg	1.518
r_mcbond_it	1.017
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.745
r_dihedral_angle_4_deg	24.013
r_dihedral_angle_3_deg	14.035
r_dihedral_angle_1_deg	5.871
r_scangle_it	3.725
r_scbond_it	2.53
r_mcangle_it	1.613
r_angle_refined_deg	1.518
r_mcbond_it	1.017
r_nbtor_refined	0.316
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.107
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5308
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
Macromolecular	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.