7NMY

Crystal structure of beta-2-microglobulin D76Y mutant

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	100 nL mother liquor / 200 nL protein 15% Glycerol, 0.1 M NaAcetate pH 4.5-5.5, 28-32%PEG 4000, 0.2 M NH4Acetate

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.706	α = 90
b = 27.691	β = 101.244
c = 64.521	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 PILATUS3 6M		2019-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.98	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.25	43.98	98	0.032	0.999	14.6	7		24565

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27	81.4		0.927	0.448	0.9	5.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YXF	1.25	43.98	24562	1211	97.81	0.181	0.1785	0.2272	19.957

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]
0.343		0.59	-0.637		0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.516
r_dihedral_angle_4_deg	15.988
r_dihedral_angle_3_deg	13.699
r_dihedral_angle_1_deg	8.703
r_lrange_it	4.209
r_lrange_other	3.672
r_scangle_it	2.852
r_scangle_other	2.848
r_scbond_it	2.428
r_scbond_other	2.417
r_mcangle_it	2.414
r_mcangle_other	2.413
r_angle_refined_deg	2.263
r_rigid_bond_restr	2.194
r_mcbond_it	1.905
r_mcbond_other	1.904
r_angle_other_deg	1.757
r_symmetry_nbd_refined	0.28
r_nbd_other	0.255
r_symmetry_nbd_other	0.226
r_symmetry_xyhbond_nbd_refined	0.224
r_xyhbond_nbd_refined	0.216
r_nbtor_refined	0.207
r_nbd_refined	0.196
r_symmetry_nbtor_other	0.111
r_chiral_restr	0.084
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	841
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data processing
Coot	model building
PHASER	phasing
XDS	data processing