9WZM | pdb_00009wzm

Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a0 domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9WZL	domain a of the same protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	2M ammonium sulfate, 0.2M lithium sulfate, 0.2M diammonium phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.773	α = 90
b = 61.773	β = 90
c = 100.761	γ = 90

Symmetry
Space Group	P 41 21 2

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		2012-10-26	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	2.1	100	98	0.049	48.8	23.8		11788

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	97.5		0.702	5.1	24.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	30.906	11708	608	97.803	0.196	0.1944	0.2044	0.2221	0.2377	RANDOM	53.576

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]
1.881			1.881		-3.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.329
r_dihedral_angle_6_deg	14.215
r_lrange_other	12.683
r_lrange_it	12.668
r_scangle_it	10.379
r_scangle_other	10.372
r_dihedral_angle_2_deg	7.459
r_mcangle_it	6.788
r_mcangle_other	6.785
r_scbond_it	6.741
r_scbond_other	6.734
r_dihedral_angle_1_deg	6.45
r_mcbond_it	4.906
r_mcbond_other	4.835
r_angle_refined_deg	1.61
r_angle_other_deg	0.541
r_nbd_refined	0.228
r_nbd_other	0.206
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.145
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_refined	0.079
r_bond_refined_d	0.007
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	917
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

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