7BGZ

Mutant L39K of recombinant beta-lactoglobulin in complex with endogenous ligand

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	3.0 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.56	α = 90
b = 53.56	β = 90
c = 110.88	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	CCD	AGILENT ATLAS CCD		2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	Agilent SuperNova	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	14.26	98.1	0.057	0.067	0.034	0.998	12.9	3.5		7446

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	97.6		0.653	0.83	0.502	0.714	1.4	2.5

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BSY	2.401	13.753	7437	1075	97.279	0.204	0.20297	0.1938	0.2663	RANDOM	50.562

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]
-0.213	-0.106		-0.213		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.42
r_dihedral_angle_3_deg	18.301
r_dihedral_angle_4_deg	8.348
r_dihedral_angle_1_deg	7.94
r_lrange_it	5.954
r_lrange_other	5.95
r_scangle_it	4
r_scangle_other	3.997
r_mcangle_it	3.972
r_mcangle_other	3.97
r_mcbond_it	2.46
r_mcbond_other	2.46
r_scbond_it	2.456
r_scbond_other	2.454
r_angle_refined_deg	1.779
r_angle_other_deg	1.233
r_nbd_other	0.243
r_symmetry_nbd_other	0.2
r_nbd_refined	0.198
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1150
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	16

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction