1S69 | pdb_00001s69

The X-ray structure of the cyanobacteria Synechocystis hemoglobin "cyanoglobin" with cyanide ligand

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	1.5M sodium citrate, 0.2M ammonium citrate, 20% sucrose, 3% dioxane, 25mM sodium cyanide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.97	68.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.06	α = 90
b = 84.06	β = 90
c = 64.62	γ = 90

Symmetry
Space Group	I 41

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	RIGAKU RAXIS IV		2002-10-01	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2002-10-02	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	ROTATING ANODE	RIGAKU	1.5418

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	1.68	32.49	75.2	0.055	15.3	4.92		37950	3	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)
1,2	1.68	1.74	5		0.343	2.1	1.02	254

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 (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1dly	1.68	32.5	3	3	37837	1053	80.46	0.19921	0.1927	0.19236	0.19	0.19921	RANDOM	28.241

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]
-0.38			-0.38		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.658
r_dihedral_angle_1_deg	5.294
r_scbond_it	3.442
r_mcangle_it	1.927
r_angle_refined_deg	1.809
r_mcbond_it	1.019
r_nbd_refined	0.229
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.197
r_symmetry_vdw_refined	0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.658
r_dihedral_angle_1_deg	5.294
r_scbond_it	3.442
r_mcangle_it	1.927
r_angle_refined_deg	1.809
r_mcbond_it	1.019
r_nbd_refined	0.229
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.197
r_symmetry_vdw_refined	0.134
r_chiral_restr	0.121
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	969
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
CRYSTAL	data reduction
d*TREK	data scaling
CNS	phasing

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.