9T6X | pdb_00009t6x

Higher-dose (676.8 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 = 28.484	α = 90
b = 35.101	β = 90
c = 123.16	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	1.103	27.743	99.9	0.161	0.194	0.076	0.995	4.9	6.4		50652

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	1.103	1.122	99.8		3.848	3.072	1.209	0.334	0.6	6.2

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	1.1	33.757	51125	999	99.754	0.164	0.1632	0.1707	0.2008	0.2064	11.88

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]
0.037			0.019		-0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.25
r_dihedral_angle_3_deg	13.418
r_dihedral_angle_2_deg	12.983
r_lrange_it	10.497
r_lrange_other	9.847
r_scangle_it	7.079
r_scangle_other	7.076
r_dihedral_angle_1_deg	4.937
r_scbond_it	4.904
r_scbond_other	4.827
r_mcangle_other	4.133
r_mcangle_it	4.119
r_rigid_bond_restr	3.66
r_mcbond_it	2.975
r_mcbond_other	2.904
r_angle_refined_deg	1.934
r_dihedral_angle_other_2_deg	1.52
r_angle_other_deg	0.732
r_symmetry_xyhbond_nbd_refined	0.319
r_xyhbond_nbd_refined	0.252
r_symmetry_nbd_refined	0.24
r_nbd_refined	0.234
r_nbd_other	0.227
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.182
r_metal_ion_refined	0.153
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.072
r_symmetry_metal_ion_refined	0.072
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1182
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	65

Software

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