7BGA | pdb_00007bga

Mutant F105A 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	2.6 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.34	α = 90
b = 53.34	β = 90
c = 112.31	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		2015-12-09	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	1.9	15.4	99.7	0.067	0.081	0.045	0.997	12	2.7		15168

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	1.9	1.95	99.8		0.492	0.651	0.419	0.677		2.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1bsy	1.9	13.789	15127	1036	99.552	0.189	0.1891	0.1854	0.2	0.2432	0.25	RANDOM	27.742

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]
0.004	0.002		0.004		-0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.223
r_dihedral_angle_4_deg	16.409
r_dihedral_angle_3_deg	13.769
r_dihedral_angle_1_deg	7.472
r_lrange_it	5.441
r_lrange_other	5.436
r_scangle_it	3.12
r_scangle_other	3.06
r_mcangle_it	2.482
r_mcangle_other	2.482
r_scbond_it	1.95
r_scbond_other	1.905
r_angle_refined_deg	1.638
r_mcbond_it	1.54
r_mcbond_other	1.54
r_angle_other_deg	1.349
r_nbd_refined	0.196
r_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.154
r_symmetry_nbd_refined	0.093
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.012
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1183
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	19

Software

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