7NMR | pdb_00007nmr

Crystal structure of beta-2-microglobulin D76S mutant

X-RAY DIFFRACTION

---

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
2.07	40.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.339	α = 90
b = 28.795	β = 96.93
c = 63.004	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	1.15	38.2	98.6	0.031	0.998	10.7	2.8		33548

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	1.15	1.17	98.4		0.916	0.504	0.8	2.8

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	1.15	38.2	33547	1675	98.526	0.15	0.1479	0.16	0.1823	0.19	20.47

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]
0.579		1.201	-1.38		0.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.846
r_dihedral_angle_4_deg	22.879
r_dihedral_angle_3_deg	11.276
r_rigid_bond_restr	9.394
r_dihedral_angle_1_deg	7.584
r_lrange_it	5.2
r_scangle_it	5.184
r_scangle_other	5.18
r_lrange_other	4.61
r_scbond_it	4.542
r_scbond_other	4.537
r_mcbond_it	3.26
r_mcangle_other	3.02
r_mcangle_it	2.966
r_mcbond_other	2.1
r_angle_refined_deg	1.893
r_angle_other_deg	1.534
r_symmetry_xyhbond_nbd_refined	0.276
r_nbd_other	0.256
r_symmetry_nbd_refined	0.236
r_xyhbond_nbd_refined	0.235
r_symmetry_nbd_other	0.196
r_nbd_refined	0.19
r_symmetry_xyhbond_nbd_other	0.185
r_nbtor_refined	0.177
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.085
r_xyhbond_nbd_other	0.083
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	818
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	18

Software

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