6FAK

Human afamin orthorhombic crystal form by controlled hydration

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	30 % PEG 1000, 270 mM CH3COONH4, 3% 6-aminohexanoic acid (ACA). 1.5 uL 5 mg/mL Stock + 1.5 uL precipitant. Streak seeding followed by micro-seeding immediately after pipetting with no pre-equilibration of the drop. Controlled hydration experiment for data collection.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.773	α = 90
b = 113.325	β = 90
c = 48.796	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS3 2M	Be CRL	2016-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.9	78.85	98.9	0.049	0.058	0.03	0.999	14.9	3.55		48102			33.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	95.8		0.868	1.031	0.547	0.728	2	3.36

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2VUE	1.9	78.85	45558	2460	98.57	0.17905	0.17686	0.219	RANDOM	44.477

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]
-1.31			-1.37		2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.615
r_dihedral_angle_4_deg	19.434
r_dihedral_angle_3_deg	16.421
r_long_range_B_refined	9.543
r_long_range_B_other	9.531
r_scangle_other	6.464
r_dihedral_angle_1_deg	5.898
r_mcangle_it	4.615
r_mcangle_other	4.615
r_scbond_it	4.228
r_scbond_other	4.212
r_mcbond_it	2.887
r_mcbond_other	2.886
r_angle_refined_deg	1.611
r_angle_other_deg	1.041
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4637
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	198

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data collection
EDNA	data collection
XSCALE	data scaling
pointless	data scaling
BALBES	phasing
ARP/wARP	model building
XDS	data reduction