1GTK

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YPN	PDB ENTRY 2YPN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.3		PROTEIN WAS CRYSTALLISED AT PH 5.3 IN SITTING DROPS OF 0.05 ML WITH 6-7 MG/ML OF PROTEIN, 0.3 MM EDTA, 15 MM DITHIOTHREITOL, 10%(W/V) PEG6000 AND 0.01% NAN3 IN 0.1 M SODIUM ACETATE.

Crystal Properties
Matthews coefficient	Solvent content
2.45	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.5	α = 90
b = 75.9	β = 90
c = 50.1	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			1997-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID09		ESRF	ID09

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	43.85	87				34417

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.75	70.7

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	PDB ENTRY 2YPN	1.66	43.85	32708	1709	87	0.2	0.198	0.247	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.704
r_scbond_it	3.14
r_angle_other_deg	2.004
r_mcangle_it	1.982
r_mcbond_it	1.174
r_dihedral_angle_3_deg	0.98
r_symmetry_vdw_refined	0.304
r_symmetry_vdw_other	0.292
r_nbd_refined	0.281
r_symmetry_hbond_refined	0.262
r_nbd_other	0.218
r_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_other	0.141
r_chiral_restr	0.117
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_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	2228
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	30

Software

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