3BJ5

Alternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295.15	2.95M Ammonium sulfate, 0.2M NaCl, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.37	α = 90
b = 57.37	β = 90
c = 68.31	γ = 120

Symmetry
Space Group	P 31 2 1

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	MARMOSAIC 225 mm CCD		2006-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.89997	EMBL/DESY, HAMBURG	X12

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	2.2	49.69	99.3	0.055	17.84	4.3	6879	6879			41.042

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	2.2	2.26	99.3		0.17	17.8	4.3	849

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	18.11	6533	344	99.29	0.19683	0.1938	0.25525	RANDOM	37.401

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]
-0.18	-0.09		-0.18		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.457
r_dihedral_angle_3_deg	19.101
r_dihedral_angle_4_deg	11.74
r_dihedral_angle_1_deg	5.882
r_scangle_it	2.841
r_scbond_it	1.76
r_angle_refined_deg	1.362
r_mcangle_it	1.286
r_mcbond_it	0.754
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.457
r_dihedral_angle_3_deg	19.101
r_dihedral_angle_4_deg	11.74
r_dihedral_angle_1_deg	5.882
r_scangle_it	2.841
r_scbond_it	1.76
r_angle_refined_deg	1.362
r_mcangle_it	1.286
r_mcbond_it	0.754
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.24
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1063
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
XDS	data scaling
MOLREP	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.