7KOT | pdb_00007kot

Energetic and structural effects of the Tanford transition on the ligand recognition of bovine 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, HANGING DROP	8	277.15	0.1 M NaCl, pH 4.5 and in 0.05 M Tris-HCl, 0.1 M NaCl, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.652	α = 90
b = 53.652	β = 90
c = 112.021	γ = 120

Symmetry
Space Group	P 32 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 PILATUS 200K		2018-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.74	46.46	99.6	0.89	83.2	14.1		19905

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.77			0.89

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	FREE R-VALUE	1BEB	1.74	46.46	19788	1012	99.592	0.195	0.1931	0.2	0.2286	0.24	32.581

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]
0.47	0.235		0.47		-1.526

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.957
r_dihedral_angle_3_deg	15.923
r_dihedral_angle_1_deg	7.571
r_lrange_it	6.645
r_lrange_other	6.608
r_dihedral_angle_4_deg	5.129
r_scangle_it	4.804
r_scangle_other	4.801
r_mcangle_it	3.538
r_mcangle_other	3.536
r_scbond_it	3.097
r_scbond_other	3.095
r_mcbond_other	2.359
r_mcbond_it	2.358
r_angle_refined_deg	2.222
r_angle_other_deg	1.497
r_symmetry_nbd_refined	0.21
r_nbd_refined	0.202
r_nbd_other	0.196
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.122
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1221
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing