8PUQ | pdb_00008puq

MetHemoglobin structure from serial synchrotron crystallography with fixed target

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SVA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	293.15	26%v PEG3350, 10mM HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.53	α = 90
b = 63.08	β = 111.02
c = 54.69	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293.15	PIXEL	DECTRIS EIGER X 16M		2021-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9762	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (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	1.95	53.55	100	0.9903	0.075	10.6	176		25258

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02			0.7593	0.4194	1.37

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	1.95	53.55	25258	1211	100	0.127	0.1252	0.14	0.1741	0.18	63.641

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]
0.398		1.89	-2.054		0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.422
r_dihedral_angle_3_deg	15.414
r_dihedral_angle_2_deg	12.253
r_lrange_other	10.449
r_lrange_it	10.448
r_scangle_other	9.661
r_scangle_it	9.654
r_scbond_it	6.95
r_scbond_other	6.93
r_dihedral_angle_1_deg	5.878
r_mcangle_it	5.156
r_mcangle_other	5.154
r_mcbond_it	4.373
r_mcbond_other	4.356
r_angle_refined_deg	2.037
r_angle_other_deg	0.843
r_nbd_refined	0.208
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.153
r_symmetry_nbd_other	0.142
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbd_refined	0.112
r_chiral_restr	0.106
r_nbd_other	0.104
r_symmetry_nbtor_other	0.068
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_gen_planes_other	0.007
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2180
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing