4M9O | pdb_00004m9o

Crystal Structure of monomeric zebrafish beta-2-microglobulin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GBL	PDB ENTRY 3GBL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate in 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.084	α = 90
b = 50.926	β = 90
c = 54.07	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315r	Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror	2011-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.14	30	98.9	0.056	0.044	27.5	5.9	6117	6117	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.17	99		0.216	0.197	6.9	5.8	300

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 3GBL	2.14	30	1	5795	5795	282	98.68	0.17486	0.17213	0.1995	0.23085	0.2185	RANDOM	27.251

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]
-0.75			1.56		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.772
r_dihedral_angle_3_deg	17.16
r_dihedral_angle_4_deg	7.927
r_dihedral_angle_1_deg	6.798
r_scangle_it	6.683
r_scbond_it	3.931
r_mcangle_it	2.368
r_angle_refined_deg	2.074
r_mcbond_it	1.194
r_chiral_restr	0.151
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	786
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling