2C19

5-(4-Carboxy-2-oxo-butylsulfanyl)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO-PENTANOIC ACID DISODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (17.0 % (W/V) PEG-3350, 120 MM NA-TARTRATE) ABOVE 500 MICROL OF RESERVOIR SOLUTION.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.203	α = 90
b = 127.203	β = 90
c = 85.848	γ = 90

Symmetry
Space Group	P 4 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	IMAGE PLATE	RIGAKU R-AXIS IV	BLUE OPTIC	2005-01-14	M	SINGLE WAVELENGTH

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

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	2.05	34.26	97.8	0.12	14.5	10.5		44731

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	2.05	2.1	97.7		0.46	0.04	9.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1B4K	2.05	89.8	41499	2220	97.8	0.147	0.144	0.201	RANDOM	18.43

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]
0.42			0.42		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.891
r_dihedral_angle_4_deg	18.916
r_dihedral_angle_3_deg	14.542
r_dihedral_angle_1_deg	6.101
r_scangle_it	3.299
r_scbond_it	2.176
r_angle_refined_deg	1.497
r_mcangle_it	1.198
r_mcbond_it	0.683
r_nbtor_refined	0.297
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.207
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5147
Nucleic Acid Atoms
Solvent Atoms	659
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling