4E8D | pdb_00004e8d

Crystal structure of streptococcal beta-galactosidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D3A

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.971	α = 90
b = 79.3	β = 106.94
c = 99.387	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2010-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9798	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	50	98.8			110056	108735		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	98.8		0.07	0.07	14.3	3.1	108735

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3D3A	1.8	46.98	108735	103282	5411	98.72	0.17556	0.17374	0.20996	0.2093	RANDOM	19.555

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]
-1.36		-0.2	1.63		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.038
r_dihedral_angle_4_deg	17.164
r_dihedral_angle_3_deg	11.46
r_dihedral_angle_1_deg	5.361
r_scangle_it	2.314
r_scbond_it	1.358
r_angle_refined_deg	0.929
r_mcangle_it	0.823
r_mcbond_it	0.41
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9697
Nucleic Acid Atoms
Solvent Atoms	871
Heterogen Atoms	78

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling