3DC8

Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YNY	1YNY, 1KCX, 1K1D
experimental model	PDB	1KCX	1YNY, 1KCX, 1K1D
experimental model	PDB	1K1D	1YNY, 1KCX, 1K1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	4.6	293	4.0M sodium formate, 0.1M sodium acetate, pH 4.6, COUNTER-DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.887	α = 90
b = 126.281	β = 90
c = 196.104	γ = 90

Symmetry
Space Group	C 2 2 21

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	BRUKER SMART 6000	Montel mirrors	2006-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.85	39.89	98.4	0.0662	13	3.47		129593			14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	89.1		0.311	3.11	1.83	8930

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	1YNY, 1KCX, 1K1D	1.85	29.6	129519	6524	98.46	0.149	0.148	0.176	RANDOM	5.383

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]
0.01			0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.226
r_dihedral_angle_4_deg	17.585
r_dihedral_angle_3_deg	11.217
r_dihedral_angle_1_deg	10.5
r_scangle_it	2.835
r_scbond_it	2.021
r_angle_refined_deg	1.644
r_mcangle_it	1.168
r_mcbond_it	0.918
r_angle_other_deg	0.332
r_nbtor_refined	0.299
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.192
r_symmetry_hbond_refined	0.187
r_chiral_restr	0.146
r_nbd_other	0.135
r_metal_ion_refined	0.056
r_bond_refined_d	0.028
r_gen_planes_refined	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7313
Nucleic Acid Atoms
Solvent Atoms	1338
Heterogen Atoms	36

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction