6TBJ | pdb_00006tbj

Structure of a beta galactosidase with inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D1I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.416	α = 89.93
b = 115.786	β = 90.08
c = 116.186	γ = 89.99

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	100	PIXEL	DECTRIS PILATUS 6M		2016-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.5	63.21	95.6	0.982	4.9	1.8		793061

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	1.5	1.53			0.585

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	4D1I	1.5	63.21	752547	40511	94.54	0.1461	0.1451	0.15	0.1644	0.16	RANDOM	20.036

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]
3.83	-0.22	1.72	-4.61	3.39	0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.099
r_dihedral_angle_4_deg	20.388
r_dihedral_angle_3_deg	13.917
r_dihedral_angle_1_deg	6.752
r_rigid_bond_restr	3.671
r_angle_refined_deg	1.837
r_angle_other_deg	1.566
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.099
r_dihedral_angle_4_deg	20.388
r_dihedral_angle_3_deg	13.917
r_dihedral_angle_1_deg	6.752
r_rigid_bond_restr	3.671
r_angle_refined_deg	1.837
r_angle_other_deg	1.566
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	33088
Nucleic Acid Atoms
Solvent Atoms	2095
Heterogen Atoms	160

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.