2GUY | pdb_00002guy

Orthorhombic crystal structure (space group P21212) of Aspergillus niger alpha-amylase at 1.6 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7TAA	PDB ENTRY 7TAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	296	30% PEG 8000, 0.2M Na-acetate, 0.1M Na-cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.799	α = 90
b = 63.228	β = 90
c = 74.456	γ = 90

Symmetry
Space Group	P 21 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		2005-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.91835	ESRF	ID23-1

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	1.59	40	98.6	0.079			65130	65130

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	1.59	1.66	90.1		0.556

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 (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 7TAA	1.59	20	60711	60711	3245	96.88	0.16527	0.16527	0.16362	0.17	0.19623	0.2	RANDOM	26.31

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]
-0.79			1.08		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.711
r_dihedral_angle_3_deg	13.725
r_dihedral_angle_4_deg	10.104
r_dihedral_angle_1_deg	5.772
r_scangle_it	2.129
r_mcangle_it	1.726
r_angle_refined_deg	1.483
r_scbond_it	1.482
r_mcbond_it	1.158
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.711
r_dihedral_angle_3_deg	13.725
r_dihedral_angle_4_deg	10.104
r_dihedral_angle_1_deg	5.772
r_scangle_it	2.129
r_mcangle_it	1.726
r_angle_refined_deg	1.483
r_scbond_it	1.482
r_mcbond_it	1.158
r_nbtor_refined	0.324
r_symmetry_hbond_refined	0.279
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.11
r_metal_ion_refined	0.03
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3686
Nucleic Acid Atoms
Solvent Atoms	564
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
SCALEPACK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.