7NMC | pdb_00007nmc

Crystal structure of beta-2-microglobulin D76E 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
2.19	43.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.63	α = 90
b = 28.871	β = 102.023
c = 67.508	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	46.6	96.3	0.046	0.994	12.5	5.6		31346

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			0.306	0.828	3.5

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	46.6	31345	1499	96.28	0.159	0.1582	0.16	0.1794	0.18	15.637

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]
0.415		0.341	-0.054		-0.465

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.001
r_dihedral_angle_4_deg	13.962
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_1_deg	7.899
r_lrange_it	4.208
r_lrange_other	3.715
r_scangle_it	3.462
r_scangle_other	3.459
r_scbond_it	2.882
r_scbond_other	2.881
r_rigid_bond_restr	2.079
r_mcangle_other	1.774
r_mcangle_it	1.769
r_angle_refined_deg	1.644
r_angle_other_deg	1.468
r_mcbond_it	1.273
r_mcbond_other	1.27
r_symmetry_nbd_refined	0.31
r_nbd_refined	0.258
r_nbd_other	0.228
r_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.174
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.025
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
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	167
Heterogen Atoms	22

Software

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