3BOA | pdb_00003boa

Crystal structure of yeast protein disulfide isomerase.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B5E	PDB ENTRY 2B5E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	100mM NaCacodylate 6.5, 0.35M MgCl2, 29% PEG2000 MME, 1mM BaCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.921	α = 90
b = 123.154	β = 90
c = 75.721	γ = 90

Symmetry
Space Group	C 2 2 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 4		2004-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

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	3.7	50	99.8	0.092	18.3	5.6		6049

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	3.7	3.76	99.7		0.696	2.1	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	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	PDB ENTRY 2B5E	3.7	19.81	5738	306	99.95	0.2442	0.23919	0.25	0.33984	0.24	RANDOM	168.842

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]
-0.32			-0.29		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.079
r_dihedral_angle_3_deg	20.373
r_dihedral_angle_4_deg	19.954
r_dihedral_angle_1_deg	8.147
r_angle_refined_deg	1.18
r_angle_other_deg	0.798
r_scangle_it	0.515
r_scbond_it	0.325
r_mcangle_it	0.296
r_mcbond_it	0.25
r_nbd_refined	0.223
r_nbtor_refined	0.185
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.172
r_symmetry_vdw_other	0.172
r_symmetry_hbond_refined	0.163
r_nbtor_other	0.084
r_chiral_restr	0.069
r_xyhbond_nbd_other	0.028
r_mcbond_other	0.024
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3864
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing