3BOM | pdb_00003bom

Crystal structure of trout hemoglobin at 1.35 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OUU	PDB entry 1OUU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	277	Protein solution (15 mg/mL CO-bound trout IV Hemoglobin, 0.025 M Sodium chloride, 0.010 M Tris-HCl pH 8.0) was mixed one to one with carbon monoxide flushed well solution to yield a final concentration of 22.5% PEG 1500 and 0.04-0.06 M MES/Acetate at pH 5.7. The solutions were pH-ed to verify that the crystallization conditions were at pH 5.7 due to the lower buffer molarity. Crystals were cryo-protected with 22.5% PEG 1500, 22.5% Ethylene glycol, 0.04-0.06 M MES/Acetate at pH 5.7 in a single step, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.455	α = 90
b = 63.162	β = 93.1
c = 78.702	γ = 90

Symmetry
Space Group	P 1 21 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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97935	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	1.35	39.294	97.4	0.118	10.482	7		120196

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	1.35	1.38	77.8		0.459	2.306	4.2	6375

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 1OUU	1.35	39.294	120109	6037	97.384	0.172	0.17	0.17	0.212	0.21	RANDOM	20.16

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]
-0.186		-0.778	-1.58		1.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.811
r_dihedral_angle_3_deg	14.47
r_dihedral_angle_4_deg	14.171
r_dihedral_angle_1_deg	4.561
r_scangle_it	3.311
r_scbond_it	2.376
r_mcangle_it	1.459
r_angle_refined_deg	1.197
r_mcbond_it	1.11
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4496
Nucleic Acid Atoms
Solvent Atoms	817
Heterogen Atoms	188

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction