7NMV

Crystal structure of beta-2-microglobulin D76Q mutant

X-RAY DIFFRACTION

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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
2.17	43.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.342	α = 90
b = 28.802	β = 102.01
c = 67.564	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 2M		2018-09-13	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)	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	1.51	46.4	95.6	0.085	0.982	7.9	2.7		15590

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	1.51	1.54	95.7		0.716	0.354	3.6	2.3

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	1.51	46.4	15588	802	95.345	0.224	0.2214	0.2662	14.384

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]
-0.345		-0.358	0.325		0.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.644
r_dihedral_angle_4_deg	22.818
r_dihedral_angle_3_deg	15.129
r_dihedral_angle_1_deg	8.11
r_lrange_it	6.076
r_lrange_other	5.878
r_scangle_it	3.628
r_scangle_other	3.621
r_scbond_it	2.266
r_scbond_other	2.266
r_mcangle_other	2.222
r_mcangle_it	2.216
r_angle_refined_deg	1.706
r_mcbond_it	1.43
r_mcbond_other	1.374
r_angle_other_deg	1.355
r_symmetry_xyhbond_nbd_refined	0.342
r_xyhbond_nbd_refined	0.268
r_symmetry_nbd_refined	0.233
r_nbd_other	0.212
r_symmetry_nbd_other	0.197
r_nbd_refined	0.189
r_nbtor_refined	0.171
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	838
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms

Software

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