1GZG

Complex of a Mg2-dependent porphobilinogen synthase from Pseudomonas aeruginosa (mutant D139N) with 5-fluorolevulinic acid

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	9		PROTEIN SOLUTION: 12 MG/ML PBGS MUTANT D139N IN 50 MM K-HEPES, 10 MM MGCL2. CRYSTALLIZATION SOLUTION: 0.99 ML PROTEIN SOLUTION = 0.01 ML 2MM 5F-LA IN 50 MM K-HEPES, 10 MM MGCL2. RESERVOIR SOLUTION: 1 M NA/K-TARTRATE, 0.2M LI2SO4, 0.1 M CHES PH = 9,5. SITTING DROP: 0.003 ML CRYSTALLISATION SOLUTION + 0.003 ML RESERVOIR SOLUTION

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.131	α = 90
b = 127.131	β = 90
c = 86.145	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	MARRESEARCH	MIRRORS	2001-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	1.66	20	99.9	0.116	11	5.2		82775		3

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	1.66	1.72	100		0.394	4.1	4.9

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1B4K	1.66	91.29	78644	4131	99.1	0.175	0.198	RANDOM	20.86

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]
0.07			0.07		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.142
r_dihedral_angle_1_deg	4.584
r_scangle_it	2.829
r_scbond_it	1.673
r_angle_refined_deg	1.657
r_mcangle_it	1.057
r_angle_other_deg	0.805
r_mcbond_it	0.581
r_xyhbond_nbd_other	0.381
r_symmetry_vdw_refined	0.361
r_nbd_refined	0.332
r_metal_ion_refined	0.232
r_symmetry_vdw_other	0.226
r_symmetry_hbond_refined	0.223
r_nbd_other	0.217
r_xyhbond_nbd_refined	0.209
r_chiral_restr	0.151
r_symmetry_hbond_other	0.02
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_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	5050
Nucleic Acid Atoms
Solvent Atoms	671
Heterogen Atoms	57

Software

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