3GYS

Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.9 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D4X	PDB ENTRY 3D4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	293	40% PEG 3350, 50mM phosphate buffer at pH 6.7, 1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.022	α = 90
b = 96.465	β = 90
c = 146.345	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MAR scanner 345 mm plate		2007-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5417

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	2.9	30	96	0.098	4.1	3.65	26800	23886	2	2

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)
	2.9	3	98.5		0.2648	1.4	3.14	2304

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3D4X	2.9	24.13	2	2	26800	23762	2656	95.99	0.19562	0.18712	0.27106	RANDOM	48.397

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			1.16		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.766
r_dihedral_angle_3_deg	21.027
r_dihedral_angle_4_deg	12.081
r_dihedral_angle_1_deg	5.972
r_angle_refined_deg	1.583
r_mcbond_it	0.818
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.291
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.248

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.766
r_dihedral_angle_3_deg	21.027
r_dihedral_angle_4_deg	12.081
r_dihedral_angle_1_deg	5.972
r_angle_refined_deg	1.583
r_mcbond_it	0.818
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.291
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.248
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.102
r_metal_ion_refined	0.022
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_mcangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8685
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	344

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.