2YXF | pdb_00002yxf

The high resolution crystal structure of beta2-microglobulin under physiological conditions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D4F	PDB ENTRY 2D4F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	288	25% PEG 4000, 25% Glycerol, 0.06M ammoniumacetate, 0.1M MOPS, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.644	α = 90
b = 28.907	β = 121.59
c = 54.397	γ = 90

Symmetry
Space Group	C 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	90	CCD	Bruker DIP-6040		2005-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.65	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.13	26.63	100	0.051	12.4	3.8	38852	38852			9.459

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.13	1.19	100		0.332	4	3.7	5630

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2D4F	1.13	26.49	38852	36904	1948	99.98	0.18436	0.1838	0.19	0.19486	0.2	RANDOM	11.113

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]
-0.38		-0.03	0.23		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.353
r_dihedral_angle_4_deg	21.752
r_dihedral_angle_3_deg	11.286
r_dihedral_angle_1_deg	6.909
r_sphericity_free	2.98
r_scangle_it	2.541
r_rigid_bond_restr	2.029
r_scbond_it	1.978
r_sphericity_bonded	1.845
r_mcangle_it	1.369
r_angle_refined_deg	1.227
r_mcbond_it	1.187
r_angle_other_deg	0.744
r_mcbond_other	0.302
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.2
r_nbd_other	0.195
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.15
r_symmetry_vdw_other	0.142
r_xyhbond_nbd_refined	0.139
r_nbtor_other	0.084
r_chiral_restr	0.08
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	828
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling