2F84 | pdb_00002f84

Crystal Structure of an orotidine-5'-monophosphate decarboxylase homolog from P.falciparum

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	298	100mM Ammonium Phosphate, 18% PEG 1000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.911	α = 90
b = 69.057	β = 90
c = 69.735	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 4		2004-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	2	69.74	96.1	0.102	0.102	4.9	3.8		22698	1	1

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	2.11	85.8		0.785	0.785	0.7	3.2	2896

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	2AQW.pdb	2.1	18.61	22698	19766	987	96.04	0.23	0.23	0.227	0.23	0.288	0.29	RANDOM	11.496

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]
-0.59			-0.28		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.745
r_dihedral_angle_4_deg	19.772
r_dihedral_angle_3_deg	15.685
r_dihedral_angle_1_deg	6.33
r_scangle_it	2.815
r_scbond_it	2.052
r_angle_refined_deg	1.475
r_mcangle_it	1.412
r_mcbond_it	0.886
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.745
r_dihedral_angle_4_deg	19.772
r_dihedral_angle_3_deg	15.685
r_dihedral_angle_1_deg	6.33
r_scangle_it	2.815
r_scbond_it	2.052
r_angle_refined_deg	1.475
r_mcangle_it	1.412
r_mcbond_it	0.886
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.216
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2662
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	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.