7EGO | pdb_00007ego

X-ray structure of the human heart fatty acid-binding protein complexed with the fluorescent probe HA527

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1M Tris-HCl (pH8.5), 50% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.521	α = 90
b = 69.657	β = 90
c = 33.844	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		2021-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.21	42.93	94.5	0.13	17.77	10.2		40169

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.21	1.28			0.5	5.1

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	3WVM	1.21	42.93	36314	1977	95.27	0.13034	0.12913	0.14	0.15159	0.16	RANDOM	12.248

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]
0.03			-0.07		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.055
r_dihedral_angle_4_deg	12.929
r_dihedral_angle_3_deg	12.257
r_dihedral_angle_1_deg	6.706
r_rigid_bond_restr	5.286
r_long_range_B_refined	2.754
r_scangle_other	2.686
r_scbond_other	2.635
r_scbond_it	2.634
r_long_range_B_other	2.585
r_angle_refined_deg	2.293
r_angle_other_deg	1.658
r_mcangle_other	1.444
r_mcangle_it	1.441
r_mcbond_it	1.387
r_mcbond_other	1.372
r_chiral_restr	0.215
r_bond_refined_d	0.022
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1036
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	45

Software

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