2GSE

Crystal Structure of Human Dihydropyrimidinease-like 2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	18% PEG 10k, 0.1M Tris, 0.2M CaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.4	α = 90
b = 126.1	β = 113
c = 102.9	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	CCD	ADSC QUANTUM 4	MIRRORS	2006-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	2.4	30	99.7	0.143	9.6	4.3	79391	79142	1	1	27.7

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)
	2.4	2.6	99.7		0.43	3.36	4.3	16757

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2.4	29.31	2	79190	75230	3960	99.96	0.173	0.169	0.17	0.245	0.25	RANDOM	18.36

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]
		0.02	-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.662
r_dihedral_angle_4_deg	18.892
r_dihedral_angle_3_deg	16.135
r_dihedral_angle_1_deg	6.572
r_scangle_it	2.586
r_scbond_it	1.697
r_angle_refined_deg	1.567
r_mcangle_it	1.153
r_angle_other_deg	0.98
r_mcbond_it	0.696
r_symmetry_vdw_other	0.217
r_nbd_refined	0.207
r_nbd_other	0.198
r_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.171
r_metal_ion_refined	0.167
r_symmetry_hbond_refined	0.139
r_mcbond_other	0.128
r_chiral_restr	0.089
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_xyhbond_nbd_other	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14638
Nucleic Acid Atoms
Solvent Atoms	849
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
MOLREP	phasing