Experiment: 5KDQ

Deoxyhemoglobin in Complex with an Aryloxyalkanoic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	6.5	298	3.2 M Sulfate/phosphate precipitant, pH 6.8, LIQUID DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.222	α = 90
b = 80.83	β = 80.77
c = 53.397	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV++		2016-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	Cu FINE FOCUS	1.54

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	2.15	29.64	96.2	0.064	21	6.75		27383

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	2.15	2.23	94.1		0.146	8.4	6.73

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	FOURIER SYNTHESIS	FREE R-VALUE	2DN2	2.15	29.64	27358	1389	96.08	0.1957	0.1924	0.1863	0.2571	0.2494	0.05

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]
-6.4449		-2.8152	10.4925		-4.0476

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.235
f_angle_d	1.284
f_chiral_restr	0.065
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4384
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	200

Software

Software
Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing