3RTO | pdb_00003rto

Acoustically mounted porcine insulin microcrystals yield an X-ray SAD structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4INS	PDB ENTRY 4INS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6		Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc sulfate) at 315K. The solution is then rapidly quenched to 293K by immersing it in a cool water bath. Quenching speed determines the resulting crystal size. 20-micron crystals are obtained by quenching in a 293K water bath, 10-micron crystals by quenching in a 283K water bath, and 5-micron crystals by quenching in ice water. pH 6.0, SMALL TUBES

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.7	α = 90
b = 81.7	β = 90
c = 33.8	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	100	CCD	ADSC QUANTUM 4		2010-04-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2010-07-30	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 315		2010-02-27	M	SINGLE WAVELENGTH
4	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2009-12-19	M	SINGLE WAVELENGTH
1,2,3,4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B		NSLS	X12B
2	SYNCHROTRON	NSLS BEAMLINE X12C		NSLS	X12C
3	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25
4	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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
1,2,3,4	1.8	50	99.8	0.114	62.2	10.5	7783	7770

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 4INS	1.8	40.85	7783	7413	357	99.83	0.18338	0.18135	0.18	0.22311	0.23	RANDOM	37.509

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	38.003
r_dihedral_angle_3_deg	17.954
r_dihedral_angle_4_deg	8.064
r_dihedral_angle_1_deg	6.773
r_scangle_it	5.716
r_scbond_it	3.423
r_angle_refined_deg	2.784
r_mcangle_it	2.626
r_mcbond_it	1.37
r_chiral_restr	0.134
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	806
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	2

Software

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