9T6Y | pdb_00009t6y

Low-dose (14.4 kGy) structure of horse-heart myoglobin at cryogenic temperature

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	3.5 M ammonium sulphate, 0.1 M Tris-HCl pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.471	α = 90
b = 35.084	β = 90
c = 123.111	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		2024-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.9795	ESRF	BM07

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	1.03	26.657	99.8	0.154	0.177	0.069	0.997	5.6	6.4		333967

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	1.03	1.111	99.5		3.823	2.643	1.027	0.379	0.7	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.03	33.741	61944	1112	99.67	0.171	0.1703	0.17	0.214	0.2167	11.607

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]
0.265			-1.599		1.334

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.781
r_dihedral_angle_3_deg	12.966
r_lrange_it	12.318
r_lrange_other	11.018
r_dihedral_angle_2_deg	10.607
r_scangle_it	6.5
r_scangle_other	6.498
r_dihedral_angle_1_deg	4.832
r_scbond_it	4.525
r_scbond_other	4.437
r_mcangle_other	4.35
r_mcangle_it	4.334
r_rigid_bond_restr	3.505
r_mcbond_it	3.046
r_mcbond_other	2.912
r_angle_refined_deg	1.897
r_dihedral_angle_other_2_deg	0.868
r_angle_other_deg	0.72
r_symmetry_xyhbond_nbd_refined	0.313
r_xyhbond_nbd_refined	0.272
r_nbd_refined	0.258
r_symmetry_nbd_refined	0.254
r_nbd_other	0.237
r_metal_ion_refined	0.185
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.183
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.074
r_symmetry_metal_ion_refined	0.013
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1188
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing