3GMF | pdb_00003gmf

Crystal structure of protein-disulfide isomerase from Novosphingobium aromaticivorans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	294	0.1M Sodium acetate pH 4.5, 3M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.526	α = 90
b = 101.526	β = 90
c = 58.413	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 315	Mirrors	2009-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

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	1.76	50.77	98.7	0.062	12.5	3.1		22299		-5	29.524

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	1.76	1.82	99.5		0.37	2	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.76	50.77	21355	714	98.97	0.18595	0.18456	0.18	0.22908	0.23	RANDOM	33.492

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]
0.08	0.04		0.08		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.047
r_dihedral_angle_3_deg	15.195
r_dihedral_angle_4_deg	12.165
r_scangle_it	7.202
r_scbond_it	5.206
r_dihedral_angle_1_deg	4.963
r_mcangle_it	4.217
r_mcbond_it	3.094
r_angle_refined_deg	1.321
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.207
r_xyhbond_nbd_refined	0.19
r_nbd_refined	0.176
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1538
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	3

Software

Software
Software Name	Purpose
ADSC	data collection
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling