6SVA | pdb_00006sva

Multicrystal structure of equine Haemoglobin at room temperature using a multilayer monochromator.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C6E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Sulphate 20% PEG 3350
2	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Sulphate 20% PEG 3350
3	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Sulphate 20% PEG 3350
4	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Sulphate 20% PEG 3350
5	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium Sulphate 20% PEG 3350
6	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M Sodium Sulphate 20% PEG 3350 0.1 M Bis Tris Propane
7	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M Sodium Sulphate 20% PEG 3350 0.1 M Bis Tris Propane

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.515	α = 90
b = 62.992	β = 111.051
c = 54.591	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER2 X 4M		2019-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.979	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.92	50.64	45.6	0.047	0.06	0.038	0.994	10.2	1.6		21606			27.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.95	9.9		0.631	0.893	0.631		1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5C6E	1.92	50.64	1.38	21606	1035	81.75	0.1424	0.1408	0.14	0.1733	0.17	35.59

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.4062
f_angle_d	1.4311
f_chiral_restr	0.0837
f_bond_d	0.0183
f_plane_restr	0.0108

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2208
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	43

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
xia2	data scaling
PHASER	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.