3GYS | pdb_00003gys

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

X-RAY DIFFRACTION

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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 (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 3D4X	2.9	24.13	2	2	26800	23762	2656	95.99	0.19562	0.18712	0.1853	0.27106	0.2674	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
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