2FTW | pdb_00002ftw

Crystal structure of dihydropyrimidinase from dictyostelium discoideum

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	25% PEG 1500, 0.1M MMT buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.6	α = 90
b = 89.599	β = 90
c = 134.953	γ = 90

Symmetry
Space Group	I 2 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	CCD	ADSC QUANTUM 4		2005-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	45.459	94.4	0.134	0.134	4.3	3.1		30568			25.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.16	94.4	94.3	0.662	0.662	0.9	2.8	30568

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1KCX	2.05	25	30551	30551	1557	93.91	0.207	0.204	0.204	0.21	0.252	0.26	RANDOM	23.157

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]
-2.63			1.37		1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.413
r_dihedral_angle_4_deg	17.318
r_dihedral_angle_3_deg	13.704
r_dihedral_angle_1_deg	5.884
r_scangle_it	1.745
r_angle_refined_deg	1.182
r_scbond_it	1.166
r_angle_other_deg	0.79
r_mcangle_it	0.708
r_mcbond_it	0.608
r_symmetry_vdw_other	0.203
r_nbd_refined	0.196
r_nbd_other	0.186
r_nbtor_refined	0.171
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.155
r_mcbond_other	0.099
r_symmetry_vdw_refined	0.085
r_nbtor_other	0.084
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_metal_ion_refined	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3748
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	9

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling