5HNR

The X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AW5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6.2 - 6.5, 1.0 - 1.6 M ammonium sulphate and 0 - 10 % dioxane.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.53	α = 90
b = 125.53	β = 90
c = 200.91	γ = 90

Symmetry
Space Group	I 4 2 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	MAR scanner 180 mm plate		1998-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.5	0.87	SRS	PX9.5

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	2.8	54.2	96	0.071	6	5.9	18652	18652			36.1

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	2.8	3	76.7		0.257	2.9	3.7

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	1aw5	2.83	44.38	17779	872	95.61	0.1687	0.1653	0.23785	RANDOM	59.13

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]
-1.04			-1.04		2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.961
r_dihedral_angle_3_deg	18.071
r_dihedral_angle_4_deg	17.986
r_long_range_B_refined	11.049
r_long_range_B_other	11.032
r_scangle_other	7.182
r_mcangle_it	6.674
r_mcangle_other	6.674
r_dihedral_angle_1_deg	6.253
r_scbond_other	4.588
r_scbond_it	4.587
r_mcbond_it	4.163
r_mcbond_other	4.159
r_angle_refined_deg	1.655
r_angle_other_deg	1.224
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4825
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling