Experiment: 4OFW

Crystal Structure of Arabidopsis thaliana DJ-1d

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5		0.1 M sodium citrate, 15% 2-propanol, 16% PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.556	α = 90
b = 115.047	β = 91.51
c = 115.531	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		PIXEL	DECTRIS PILATUS 2M-F		2011-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A		Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.3	50	95.9	0.11	0.11	14.6	4.5		117444

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	2.3	2.38	90.1		0.345		2.7	10934

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1PDV	2.3	50	117422	11742	95.9	0.2428	0.2427	0.284	0.2838	32.1717

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]
-9.915		-2.573	-5.585		15.5

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.775
c_mcangle_it	2.033
c_scbond_it	1.864
c_angle_d	1.318
c_mcbond_it	1.224
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17544
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
Coot	model building
SCALEPACK	data scaling