7NMT | pdb_00007nmt

Crystal structure of beta-2-microglobulin D76G 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
2.08	40.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.542	α = 90
b = 28.683	β = 98.466
c = 62.473	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	1.2	44.43	98.4	0.037	0.997	10.7	2.6		30235

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	98.4		0.219	0.911	2.9	2.6

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	44.43	30234	1517	98.188	0.141	0.1388	0.15	0.174	0.18	15.912

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]
0.025		-0.039	-1.222		1.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.261
r_dihedral_angle_4_deg	15.528
r_dihedral_angle_3_deg	10.658
r_rigid_bond_restr	9.586
r_dihedral_angle_1_deg	7.952
r_lrange_it	4.878
r_scangle_it	4.568
r_scangle_other	4.568
r_lrange_other	4.256
r_scbond_it	3.825
r_scbond_other	3.824
r_mcangle_it	2.619
r_mcangle_other	2.617
r_angle_refined_deg	2.139
r_mcbond_other	1.951
r_mcbond_it	1.949
r_angle_other_deg	1.576
r_symmetry_nbd_refined	0.303
r_xyhbond_nbd_refined	0.285
r_symmetry_xyhbond_nbd_refined	0.263
r_nbd_other	0.241
r_nbd_refined	0.191
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.173
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	833
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms

Software

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