3GQP | pdb_00003gqp

Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.0 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	7	293	50% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.507	α = 90
b = 73.217	β = 103.38
c = 70.38	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2008-02-29	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 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	30	93.8	0.0739	5.1	2.5	35212	33292	2.3	2.3

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)
	2	2.07	92.2		0.3237	1.2	2.55	2785

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	29.72	2.3	2.3	35212	31437	3460	93.89	0.25317	0.24826	0.25	0.29806	0.26	RANDOM	26.551

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]
-0.6		0.12	-0.13		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.516
r_dihedral_angle_3_deg	17.118
r_dihedral_angle_4_deg	12.785
r_dihedral_angle_1_deg	5.834
r_scangle_it	2.393
r_scbond_it	1.763
r_angle_refined_deg	1.367
r_mcangle_it	1.017
r_mcbond_it	0.729
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.516
r_dihedral_angle_3_deg	17.118
r_dihedral_angle_4_deg	12.785
r_dihedral_angle_1_deg	5.834
r_scangle_it	2.393
r_scbond_it	1.763
r_angle_refined_deg	1.367
r_mcangle_it	1.017
r_mcbond_it	0.729
r_nbtor_refined	0.292
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4404
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	172

Software

Software
Software Name	Purpose
MAR345dtb	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.