5SY6 | pdb_00005sy6

Atomic resolution structure of human DJ-1, DTT bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P5F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	23-27% PEG 3000, 100 mM HEPES, 200 mM NaCl, 10 mM dithiothreitol (DTT)

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.227	α = 90
b = 75.227	β = 90
c = 75.227	γ = 120

Symmetry
Space Group	P 31 2 1

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 315	bent conical Si, Rh coated	2006-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.15	49	100	0.088	1	16.3	11.1		87636

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.17	99.7		1.667	0.614	1.7	8.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1P5F	1.15	49	83306	4296	99.99	0.11067	0.10971	0.11	0.12948	0.13	RANDOM	18.749

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]
-0.04	-0.02		-0.04		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	51.923
r_dihedral_angle_2_deg	34.166
r_dihedral_angle_4_deg	20.794
r_sphericity_bonded	15.704
r_dihedral_angle_3_deg	11.062
r_long_range_B_refined	7.322
r_long_range_B_other	7.32
r_dihedral_angle_1_deg	5.929
r_scangle_other	3.549
r_scbond_it	3.113
r_scbond_other	3.112
r_rigid_bond_restr	2.746
r_mcangle_other	2.589
r_mcangle_it	2.588
r_mcbond_other	1.913
r_mcbond_it	1.905
r_angle_refined_deg	1.675
r_angle_other_deg	1.041
r_chiral_restr	0.117
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1374
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing