2B5E | pdb_00002b5e

Crystal Structure of Yeast Protein Disulfide Isomerase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	sodium cacodylate, magnesium chloride, PEG 2000 MME, barium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.56	α = 90
b = 136.56	β = 90
c = 69.524	γ = 90

Symmetry
Space Group	I 4

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 315		2005-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50					24847

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	2.4	20	23557	1246	98.7	0.193	0.191	0.2101	0.246	0.2048	RANDOM	66.965

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]
-1.75			-1.75		3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.729
r_dihedral_angle_4_deg	19.371
r_dihedral_angle_3_deg	18.08
r_dihedral_angle_1_deg	8.219
r_scangle_it	2.7
r_scbond_it	1.758
r_angle_refined_deg	1.624
r_mcangle_it	1.093
r_angle_other_deg	0.883
r_mcbond_it	0.854
r_xyhbond_nbd_other	0.29
r_symmetry_hbond_refined	0.264
r_symmetry_vdw_other	0.234
r_xyhbond_nbd_refined	0.231
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.223
r_nbd_other	0.186
r_nbtor_refined	0.186
r_mcbond_other	0.145
r_chiral_restr	0.097
r_nbtor_other	0.091
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3820
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	13

Software

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