1YUP | pdb_00001yup

Reindeer beta-lactoglobulin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BEB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	2.6M Na malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.24	α = 90
b = 94.14	β = 105.76
c = 64.15	γ = 90

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.731140	ESRF	ID29

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	1BEB	2.1	19.96	63710	60524	3186	100	0.23879	0.23503	0.24	0.31144	0.3	RANDOM	33.539

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]
-0.09	0.18	3.87	-3.51	0.01	5.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.197
r_scangle_it	2.8
r_scbond_it	1.704
r_angle_refined_deg	1.558
r_mcangle_it	1.281
r_angle_other_deg	0.911
r_mcbond_it	0.693
r_symmetry_hbond_refined	0.266
r_symmetry_vdw_refined	0.26
r_nbd_other	0.249
r_nbd_refined	0.222
r_symmetry_vdw_other	0.217
r_xyhbond_nbd_refined	0.203
r_nbtor_other	0.149
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9684
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
MOLREP	phasing