4ZGG | pdb_00004zgg

Crystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	5.00% polyethylene glycol 6000, 0.1M TRIS pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.002	α = 90
b = 75.002	β = 90
c = 74.897	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	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2014-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1		SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.23	29.796	98.3	0.115	0.124	0.046	8.1	6.9	69760	69760

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.26	86.1		0.804	0.804	0.913	0.422	0.9	4.1	4473

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.23	29.796	69700	3374	98.23	0.1172	0.1164	0.1526	0.1339	0.1675	RANDOM	17.4434

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]
0.2	0.1		0.2		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.157
r_sphericity_free	30.129
r_dihedral_angle_4_deg	19.353
r_dihedral_angle_3_deg	11.474
r_sphericity_bonded	8.773
r_dihedral_angle_1_deg	6.157
r_rigid_bond_restr	2.717
r_mcbond_it	2.064
r_mcangle_it	2.034
r_mcbond_other	1.992
r_angle_refined_deg	1.697
r_angle_other_deg	1.091
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1396
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	40

Software

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