3HG4 | pdb_00003hg4

Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R46	human alpha-galactosidase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.218	α = 90
b = 90.218	β = 90
c = 216.615	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	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic Blue		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	2.3	50	99.7	0.112	0.112	28.328	15.9		46337			51.2

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)
1	2.3	2.38	100		0.944	0.944	3.4	16	4548

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	FOURIER SYNTHESIS	THROUGHOUT	human alpha-galactosidase	2.3	18.05	46268	949	99.86	0.166	0.165	0.2113	0.221	0.2585	RANDOM	49.847

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.363
r_dihedral_angle_3_deg	14.292
r_dihedral_angle_4_deg	13.572
r_dihedral_angle_1_deg	5.882
r_scangle_it	1.828
r_angle_refined_deg	1.159
r_scbond_it	1.058
r_mcangle_it	0.609
r_mcbond_it	0.375
r_nbtor_refined	0.306
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.168
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6261
Nucleic Acid Atoms
Solvent Atoms	682
Heterogen Atoms	307

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling