3LRL | pdb_00003lrl

Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae with melibiose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Deglycosylated sample. 19% PEG3350, 0.1 M BisTris, 0.2 M SCNK, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.729	α = 90
b = 100.729	β = 90
c = 111.28	γ = 90

Symmetry
Space Group	P 4 21 2

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	ADSC QUANTUM 315		2009-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2.4	111.28	99.6	0.111	0.111	6.7	10.4		22940			32.2

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)
	2.4	2.53	99.2		0.433	0.433	5.8	10.1	3262

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	PDB ENTRY 1UAS	2.4	59.99	21747	1174	99.47	0.20131	0.19849	0.2001	0.25336	0.2498	RANDOM	26.253

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]
0.73			0.73		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.826
r_dihedral_angle_4_deg	19.22
r_dihedral_angle_3_deg	15.453
r_dihedral_angle_1_deg	6.121
r_scangle_it	2.806
r_scbond_it	1.931
r_angle_refined_deg	1.546
r_mcangle_it	1.163
r_mcbond_it	0.608
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3518
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	136

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling