2BMB

X-ray structure of the bifunctional 6-hydroxymethyl-7,8- dihydroxypterin pyrophosphokinase dihydropteroate synthase from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EYE	PDB ENTRY 1EYE, PDB ENTRY 1CBK
experimental model	PDB	1CBK	PDB ENTRY 1EYE, PDB ENTRY 1CBK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		1.17 M NAH2PO4, 0.63 M K2HPO4, PH 6.3

Crystal Properties
Matthews coefficient	Solvent content
3.44	63.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.566	α = 90
b = 92.566	β = 90
c = 192.401	γ = 90

Symmetry
Space Group	P 41 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	113	IMAGE PLATE	RIGAKU IMAGE PLATE	AXCO MONOCAPILLARY OPTICS	2003-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.3	40	99.1	0.17	22.4	10.7		37688

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	2.3	2.34	91.1		0.85	3.8	2

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 1EYE, PDB ENTRY 1CBK	2.3	40	35738	1877	99.1	0.18	0.178	0.216	RANDOM	32.76

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]
-0.13			-0.13		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.942
r_dihedral_angle_4_deg	19.109
r_dihedral_angle_3_deg	15.776
r_dihedral_angle_1_deg	5.77
r_scangle_it	5.433
r_mcangle_it	4.402
r_scbond_it	3.883
r_mcbond_it	3.111
r_angle_refined_deg	1.212
r_nbtor_refined	0.299
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.174
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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	4094
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	36

Software

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