9WZL | pdb_00009wzl

Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9WZK	inactive mutant

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 = 33.724	α = 90
b = 174.375	β = 103.08
c = 53.015	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 210r		2012-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.1	100	100	0.151	11.2	7.1		34783

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	2.1	2.18	100		0.69	3.3	7.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	32.281	34627	1742	99.965	0.193	0.1902	0.1982	0.2528	0.2598	RANDOM	28.138

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]
-0.037		-0.084	0.063		0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.556
r_dihedral_angle_6_deg	13.241
r_lrange_it	7.178
r_lrange_other	7.177
r_dihedral_angle_1_deg	6.691
r_dihedral_angle_2_deg	6.458
r_scangle_it	5.511
r_scangle_other	5.51
r_mcangle_it	3.912
r_mcangle_other	3.912
r_scbond_it	3.49
r_scbond_other	3.489
r_mcbond_it	2.709
r_mcbond_other	2.708
r_angle_refined_deg	1.752
r_angle_other_deg	0.58
r_nbd_refined	0.219
r_nbd_other	0.202
r_symmetry_nbd_other	0.2
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.185
r_symmetry_nbd_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_other	0.104
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3918
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	28

Software

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