7L3Y | pdb_00007l3y

Crystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H sperm whale myoglobin; partial occupancy)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FWX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.6	277	1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000. After crystalization, soaked, under anaerobic conditions, in 20 mM dithionite for 10 minutes, and washed with anaerobic buffer. Reduced crystals were sealed in an air-tight bomb and pressurized at ~1500 psi O2 for up to 10 minutes. Crystals were harvested and cryocooled after a brief soak in 50% PEG 400 supersaturated with O2.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.845	α = 90
b = 46.982	β = 90
c = 78.034	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	100	PIXEL	DECTRIS PILATUS 6M		2015-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.98	SSRL	BL11-1

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	1.18	39.02	97	0.024	0.028	0.013	1	31.7	3.9		47352

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.2	63.4		0.216	0.275	0.169	0.902		2.1

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	4FWX	1.18	39.02	1.34	86347	4119	92.81	0.1582	0.1566	0.16	0.1902	0.19	17.26

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	14.941
f_angle_d	1.3967
f_chiral_restr	0.1015
f_bond_d	0.0127
f_plane_restr	0.0107

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1219
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	46

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	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.