5YL3 | pdb_00005yl3

Crystal structure of horse heart myoglobin reconstituted with manganese porphycene in resting state at pH 8.5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WI8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Hanging drop containing 1.5 M ammonium sulfate, 5 mg/mL of protein, 50 mM Tris-HCl and 5 mM potassium phosphate at pH 8.5 was equilibrated with the reserver solution containing 3.0 M ammonium sulfate and 100 mM Tris-HCl buffer at pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.575	α = 90
b = 28.706	β = 106.15
c = 62.702	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	CCD	RIGAKU SATURN A200	mirrors	2014-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.00	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.5	50	99.6	0.073	0.078	0.029	11.1	7		19335

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	1.5	1.53	93.8		0.526	0.584	0.249	0.851		5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3WI8	1.5	30	17192	937	94.19	0.1704	0.1683	0.18	0.2077	0.21	RANDOM	15.996

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]
0.14		0.12	-0.04		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.833
r_dihedral_angle_4_deg	19.285
r_dihedral_angle_3_deg	13.916
r_dihedral_angle_1_deg	4.989
r_angle_refined_deg	2.947
r_angle_other_deg	1.065
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.833
r_dihedral_angle_4_deg	19.285
r_dihedral_angle_3_deg	13.916
r_dihedral_angle_1_deg	4.989
r_angle_refined_deg	2.947
r_angle_other_deg	1.065
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1185
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	58

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
REFMAC	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.