8PUR | pdb_00008pur

DexyHemoglobin 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	1IBE

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
2.8	56.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.29	α = 90
b = 63.06	β = 111.01
c = 54.75	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		2021-03-07	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)	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	1.85	53.504	100	0.9914	12.48	205		29515

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.916			0.9049	2.9

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	1.85	53.504	29515	1474	100	0.132	0.1299	0.14	0.1622	0.17	70.77

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]
0.493		1.674	-1.483		-0.228

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.925
r_dihedral_angle_3_deg	14.561
r_dihedral_angle_2_deg	12.972
r_lrange_other	12.391
r_lrange_it	12.388
r_scangle_other	11.722
r_scangle_it	11.719
r_scbond_it	8.357
r_scbond_other	8.348
r_mcangle_it	6.576
r_mcangle_other	6.575
r_dihedral_angle_1_deg	5.491
r_mcbond_it	5.376
r_mcbond_other	5.365
r_angle_refined_deg	2.03
r_angle_other_deg	0.905
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.139
r_symmetry_nbd_other	0.129
r_chiral_restr	0.113
r_symmetry_nbd_refined	0.11
r_nbd_other	0.066
r_symmetry_nbtor_other	0.062
r_bond_refined_d	0.014
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	2190
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	86

Software

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