3GXN | pdb_00003gxn

Crystal structure of apo alpha-galactosidase A at pH 4.5

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION			vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.375	α = 90
b = 90.375	β = 90
c = 217.524	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	3.01	78					18676

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	3.01	44.66	18676	971	88.08	0.239	0.236	0.2294	0.301	0.2924	RANDOM	121.193

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]
4.48	2.24		4.48		-6.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.224
r_dihedral_angle_3_deg	23.591
r_dihedral_angle_4_deg	23.071
r_dihedral_angle_1_deg	7.568
r_angle_refined_deg	1.844
r_scangle_it	1.606
r_scbond_it	1.033
r_mcangle_it	0.63
r_symmetry_vdw_refined	0.484
r_mcbond_it	0.388
r_symmetry_hbond_refined	0.37
r_nbtor_refined	0.328
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.126
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6244
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction