1KWF | pdb_00001kwf

Atomic Resolution Structure of an Inverting Glycosidase in Complex with Substrate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.336	α = 90
b = 62.767	β = 90
c = 103.493	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	IMAGE PLATE	MARRESEARCH		1996-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8815	EMBL/DESY, HAMBURG	BW7B

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	0.94	30	99.8	0.043			208140	208140

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)
	0.94	0.95	97.7		0.19

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		FREE R	0.94	10	197438	10391	94.8	0.094		0.113	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
132	2644	3345.45

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.129
s_non_zero_chiral_vol	0.121
s_zero_chiral_vol	0.115
s_similar_adp_cmpnt	0.042
s_anti_bump_dis_restr	0.041
s_from_restr_planes	0.03
s_angle_d	0.027
s_bond_d	0.014
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2994
Nucleic Acid Atoms
Solvent Atoms	499
Heterogen Atoms	90

Software

Software
Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	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.