7NMO | pdb_00007nmo

Crystal structure of beta-2-microglobulin D76A mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.09	41.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.665	α = 90
b = 28.799	β = 98.41
c = 62.289	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	0.9686	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	1.2	44.41	97.7	0.014	0.999	32.4	6.3		30020

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	1.2	1.22	92.3		0.066	0.988	10.2	5.2

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	THROUGHOUT	2YXF	1.2	44.41	30020	1506	97.234	0.131	0.13	0.13	0.1586	0.16	16.658

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]
-0.22		0.12	0.418		-0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.892
r_dihedral_angle_4_deg	13.452
r_dihedral_angle_3_deg	12.06
r_rigid_bond_restr	10.286
r_dihedral_angle_1_deg	7.696
r_scbond_it	7.644
r_scbond_other	7.643
r_lrange_it	7.04
r_lrange_other	6.986
r_scangle_it	5.289
r_scangle_other	5.289
r_angle_refined_deg	2.188
r_mcangle_other	2.145
r_mcangle_it	2.144
r_mcbond_it	1.592
r_mcbond_other	1.582
r_angle_other_deg	1.556
r_symmetry_xyhbond_nbd_refined	0.325
r_xyhbond_nbd_refined	0.237
r_nbd_refined	0.228
r_symmetry_nbd_other	0.209
r_symmetry_nbd_refined	0.188
r_xyhbond_nbd_other	0.185
r_nbtor_refined	0.18
r_chiral_restr	0.155
r_nbd_other	0.152
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	834
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms

Software

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