7AAE | pdb_00007aae

Crystal structure of Human serum albumin in complex with myristic acid at 2.27 Angstrom Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	50 mM HEPES, 50 mM MOPS, 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.315	α = 90
b = 38.537	β = 104.45
c = 184.28	γ = 90

Symmetry
Space Group	I 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	100	PIXEL	DECTRIS EIGER X 16M		2019-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.27	29.23	99.5	0.06	0.999	15.28	5.5		30458

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27	2.35			0.583	0.866	2.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1bj5	2.27	29.228	30458	1502	99.516	0.227	0.2237	0.22	0.2907	0.29	61.474

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]
-0.101		-0.054	0.131		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.859
r_dihedral_angle_4_deg	22.092
r_dihedral_angle_3_deg	19.456
r_lrange_it	10.061
r_scangle_it	7.473
r_mcangle_it	6.599
r_dihedral_angle_1_deg	6.085
r_scbond_it	4.844
r_mcbond_it	4.509
r_angle_refined_deg	1.859

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.859
r_dihedral_angle_4_deg	22.092
r_dihedral_angle_3_deg	19.456
r_lrange_it	10.061
r_scangle_it	7.473
r_mcangle_it	6.599
r_dihedral_angle_1_deg	6.085
r_scbond_it	4.844
r_mcbond_it	4.509
r_angle_refined_deg	1.859
r_nbtor_refined	0.3
r_symmetry_xyhbond_nbd_refined	0.268
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4622
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.