9WZK | pdb_00009wzk

Crystal structure of the inactive mutant of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domains

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.169	α = 90
b = 171.462	β = 106.268
c = 52.726	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	95	CCD	ADSC QUANTUM 315r		2011-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	1.8	100	96.8	0.063	18.9	6.1		53646

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	1.8	1.86	99.1		0.91	2.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	28.33	53458	2710	96.695	0.224	0.2213	0.2213	0.2655	0.2656	RANDOM	43.887

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]
0.019		-0.009	-0.023		0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.62
r_dihedral_angle_6_deg	11.818
r_lrange_it	8.074
r_dihedral_angle_1_deg	6.431
r_dihedral_angle_2_deg	6.431
r_scangle_it	5.574
r_mcangle_it	4.606
r_scbond_it	3.602
r_mcbond_it	3.066
r_angle_refined_deg	1.504
r_nbtor_refined	0.31
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.199
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.113
r_gen_planes_refined	0.007
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3888
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing