2F6D | pdb_00002f6d

Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AYX	pdb entry 1AYX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	295	50 mM acetate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.58	α = 90
b = 85.35	β = 90
c = 97.51	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	AREA DETECTOR	MARRESEARCH	mirrors	2002-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9096	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	10	94.5	0.043	17.5	3.49		59266	1	1	15.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.62			0.144	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1AYX	1.6	10	2	56255	3010	94.04	0.12	0.11975	0.11762	0.14	0.15958	0.17	RANDOM	12.659

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]
-0.21			0.48		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.733
r_scangle_it	3.318
r_sphericity_free	2.593
r_scbond_it	2.237
r_sphericity_bonded	1.82
r_angle_refined_deg	1.609
r_mcangle_it	1.535
r_rigid_bond_restr	1.184
r_angle_other_deg	1.047
r_mcbond_it	0.938
r_symmetry_vdw_other	0.274
r_nbd_other	0.248
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.21
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.159
r_nbtor_other	0.085
r_gen_planes_refined	0.015
r_gen_planes_other	0.015
r_bond_refined_d	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3870
Nucleic Acid Atoms
Solvent Atoms	810
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing