3OBK | pdb_00003obk

Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii ME49 in complex with the reaction product porphobilinogen

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B4K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	90% PACT SCREEN CONDITION E4 + 10% ADDIT SCREEN D7: 0.18 M KSCN, 18% PEG 3350, 3% W/V DIAMINOOCTANE, 5 MM AMINOLEVULINIC ACID, TOGOA.17087.A.Y2 AT 6.3 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 7.00, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.11	α = 90
b = 187.17	β = 90
c = 95.86	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		2010-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	ALS	5.0.2

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	2.5	49.93	98.6	0.115	11.8	4.04	110745	109171		-3	31.45

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	2.5	2.56	90.3		0.538	2.3	3.56

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	1B4K	2.5	49.93	110745	108861	5439		0.18	0.18	0.177	0.18	0.232	0.23	RANDOM	23.16

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]
1.7			-1.25		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.506
r_dihedral_angle_4_deg	20.266
r_dihedral_angle_3_deg	15.417
r_dihedral_angle_1_deg	6.107
r_scangle_it	2.816
r_scbond_it	1.678
r_angle_refined_deg	1.497
r_mcangle_it	0.974
r_angle_other_deg	0.928
r_mcbond_it	0.503
r_mcbond_other	0.123
r_chiral_restr	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21476
Nucleic Acid Atoms
Solvent Atoms	586
Heterogen Atoms	228

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling