6NKQ | pdb_00006nkq

The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8

X-RAY DIFFRACTION

---

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	3.8	293	Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.888	α = 90
b = 114.121	β = 90
c = 140.506	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	173	PIXEL	DECTRIS PILATUS 300K		2018-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	.987	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.2	60	94	0.205	0.19	0.209	0.031	0.999	10.7	45.2		49538			93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.7	45.3		1.62	1.62	1.66	0.24	0.976	3.4	46.7

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 (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	2.3	57.06	43606	2327	99.46	0.20974	0.20681	0.21	0.26097	0.26	RANDOM	92.982

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]
110.93		-1.74	18.76		-129.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.383
r_long_range_B_refined	15.927
r_long_range_B_other	15.926
r_dihedral_angle_4_deg	15.919
r_dihedral_angle_3_deg	15.061
r_mcangle_it	11.171
r_mcangle_other	11.17
r_scangle_other	9.357
r_mcbond_other	8.173
r_mcbond_it	8.172
r_dihedral_angle_1_deg	7.779
r_scbond_it	6.792
r_scbond_other	6.791
r_angle_refined_deg	1.109
r_angle_other_deg	1.022
r_chiral_restr	0.028
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_gen_planes_other	0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7519
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing