7NN5 | pdb_00007nn5

Crystal structure of beta-2-microglobulin D76K 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
1.81	31.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.43	α = 90
b = 27.721	β = 96.692
c = 60.048	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	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	1.24	41.24	97.2	0.034	0.999	13.2	3.7		23336

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	1.24	1.26	72.4		0.405	0.691	1.8	2.7

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	1.242	41.24	23332	1147	97.132	0.194	0.1922	0.2	0.2301	0.23	12.336

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]
0.818		-1.21	-0.666		0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.266
r_dihedral_angle_4_deg	20.126
r_dihedral_angle_3_deg	12.675
r_dihedral_angle_1_deg	9.422
r_rigid_bond_restr	5.69
r_lrange_it	3.257
r_lrange_other	2.699
r_angle_refined_deg	2.418
r_scangle_it	2.128
r_scangle_other	2.123
r_scbond_it	2.041
r_scbond_other	2.03
r_angle_other_deg	1.982
r_mcangle_other	1.79
r_mcangle_it	1.787
r_mcbond_it	1.616
r_mcbond_other	1.503
r_symmetry_xyhbond_nbd_refined	0.289
r_nbd_other	0.252
r_symmetry_nbd_other	0.236
r_nbtor_refined	0.218
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.186
r_symmetry_nbd_refined	0.181
r_symmetry_nbtor_other	0.114
r_chiral_restr	0.11
r_bond_refined_d	0.033
r_bond_other_d	0.018
r_gen_planes_refined	0.013
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	829
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms

Software

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