4I6X

Crystal Structure of Non-catalyic Domain of Protein Disulfide Isomerase-related (PDIr) Protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	0.15 M DL-malic acid, 20% PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.686	α = 90
b = 41.265	β = 90
c = 90.893	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 210		2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9770	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.5	50	95.08	0.031	43.5	5.7	20332	19332	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	67.01		0.268	3.6	4.1	972

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.5	45.45	1	1	20332	19332	1050	95.08	0.1933	0.19117	0.23681	RANDOM	25.386

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]
0.62			-0.18		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.659
r_dihedral_angle_4_deg	22.519
r_dihedral_angle_3_deg	14.033
r_dihedral_angle_1_deg	4.69
r_scangle_it	3.327
r_scbond_it	2.062
r_mcangle_it	1.29
r_angle_refined_deg	1.17
r_mcbond_it	0.817
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.659
r_dihedral_angle_4_deg	22.519
r_dihedral_angle_3_deg	14.033
r_dihedral_angle_1_deg	4.69
r_scangle_it	3.327
r_scbond_it	2.062
r_mcangle_it	1.29
r_angle_refined_deg	1.17
r_mcbond_it	0.817
r_nbtor_refined	0.307
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.162
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	936
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.