2FDS | pdb_00002fds

Crystal Structure of Plasmodium Berghei Orotidine 5'-monophosphate Decarboxylase (ortholog of Plasmodium falciparum PF10_0225)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AQW	PDB Entry: 2AQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	16% Peg3350, 140mM diammonium hydrogen citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.202	α = 90
b = 108.623	β = 97.3
c = 69.89	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	IMAGE PLATE	RIGAKU RAXIS IV		2005-10-31		SINGLE WAVELENGTH
2	1	x-ray

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.72	50	94.4	0.047		3		65456

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.72	1.78	67		0.382		1.9	4637

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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: 2AQW	1.72	29.22	65422	3308	94.27	0.188	0.186	0.18	0.221	0.22	RANDOM	25.168

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			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.674
r_dihedral_angle_4_deg	17.932
r_dihedral_angle_3_deg	13.629
r_dihedral_angle_1_deg	5.715
r_mcangle_it	2.034
r_scangle_it	2.028
r_scbond_it	1.374
r_angle_refined_deg	1.314
r_mcbond_it	1.276
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.674
r_dihedral_angle_4_deg	17.932
r_dihedral_angle_3_deg	13.629
r_dihedral_angle_1_deg	5.715
r_mcangle_it	2.034
r_scangle_it	2.028
r_scbond_it	1.374
r_angle_refined_deg	1.314
r_mcbond_it	1.276
r_nbtor_refined	0.306
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.105
r_symmetry_hbond_refined	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5438
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.