7C62 | pdb_00007c62

The Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.1 M DL-Malic acid pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.74	59.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.57	α = 90
b = 74.57	β = 90
c = 74.956	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	RIGAKU SATURN 944+		2020-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	2.027	50	99.8	0.109	19.1	8		16019

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)
1	2.03	2.07			0.506

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1pdv	2.027	26.446	16005	847	99.732	0.153	0.152	0.16	0.1736	0.18	27.223

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]
0.486	0.243		0.486		-1.577

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.381
r_dihedral_angle_4_deg	19.732
r_dihedral_angle_3_deg	12.934
r_dihedral_angle_1_deg	6.613
r_lrange_it	4.185
r_lrange_other	4.003
r_scangle_it	2.354
r_scangle_other	2.353
r_mcangle_it	1.561
r_mcangle_other	1.56
r_scbond_it	1.432
r_scbond_other	1.431
r_angle_refined_deg	1.236
r_angle_other_deg	1.195
r_mcbond_it	0.949
r_mcbond_other	0.94
r_nbd_other	0.198
r_symmetry_nbd_refined	0.195
r_nbd_refined	0.185
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.135
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.052
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1375
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing