2Q8L | pdb_00002q8l

Crystal structure of orotidine 5'-phosphate decarboxylase from Plasmodium falciparum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F84	PDB entry 2F84

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	15% PEG 10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.563	α = 90
b = 70.909	β = 90
c = 70.201	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		2006-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.978565	APS	19-ID

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	2.1	24.95	97.15	0.065	0.065	11.8	9.3	19423	19423

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	2.1	2.14	100		0.267	0.267	7.39	9.6	1015

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2F84	2.1	24.95	19423	19423	597	97.15	0.21746	0.21746	0.21643	0.24929	0.2385	RANDOM	35.622

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]
-1.77			-0.11		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.853
r_dihedral_angle_4_deg	23.714
r_dihedral_angle_3_deg	18.192
r_dihedral_angle_1_deg	7.315
r_scangle_it	3.467
r_scbond_it	2.729
r_mcangle_it	1.618
r_angle_refined_deg	1.464
r_mcbond_it	1.258
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.212
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.117
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2593
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing