8ZRZ | pdb_00008zrz

The 1.26 angstrom resolution structure of Bacillus cereus beta-amylase in complex with maltose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B9Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	HANGING DROP VAPOR DIFFUSION AGAINST 0.1 M PHOSPHATE BUFFER PH 6.5, 15% PEG 6000 AND 5% SATN. AMMONIUM SULFATE WITH A PROTEIN CONCENTRATION OF 15MG/ML.

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.974	α = 90
b = 89.843	β = 103.09
c = 66.035	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 4r		2002-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.26	50	99.3	0.047	0.054	0.995	48.5	3.3		171593		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.26	1.28	80.5		0.182	0.246	0.946	5.95	1.7

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.26	10	162442	8573	93.4	0.124	0.1215	0.1645	0.1581	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
69		5150.4

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.38
s_approx_iso_adps	0.1605
s_similar_adp_cmpnt	0.0481
s_anti_bump_dis_restr	0.0472
s_angle_d	0.0318
s_bond_d	0.0143
s_from_restr_planes	0.006
s_similar_dist
s_zero_chiral_vol
s_rigid_bond_adp_cmpnt

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4371
Nucleic Acid Atoms
Solvent Atoms	887
Heterogen Atoms	222

Software

Software
Software Name	Purpose
PHENIX	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.