Experiment: 5O41

Low-dose fixed target serial synchrotron crystallography structure of sperm whale myoglobin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES		293	Tris, HCl, ammonium sulfate, CO

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.873	α = 90
b = 46.876	β = 90
c = 84.665	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	PIXEL	DECTRIS PILATUS3 6M		2016-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	42.35	100	0.7947	0.936	4.27	25.3		14552

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		0.9256	0.475	0.36	18.3

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	1a6m	1.8	42.333	1.34	14539	1454	99.88	0.2006	0.1948	0.1942	0.2532	0.255

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	8.106
f_angle_d	1.324
f_chiral_restr	0.065
f_bond_d	0.017
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1225
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	55

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
cctbx.prime	data scaling
PHASER	phasing