1C7S | pdb_00001c7s

BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8		CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.794	α = 90
b = 99.96	β = 90
c = 86.308	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	IMAGE PLATE	MARRESEARCH	345 MM IMAGE PLATE	1999-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		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	1.8	15	96.9	0.024	32832			76047

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)
	1.8	1.86	90.8		0.095	4738

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	R-FREE	PDB ENTRY 1QBB	1.8	15	76047	7659	86.9	0.183	0.171	0.18	0.224	0.22	RANDOM	21.8

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_staggered_tor	15
p_planar_tor	3.5
p_scangle_it	3.496
p_scbond_it	2.584
p_mcangle_it	2.016
p_mcbond_it	1.481
p_multtor_nbd	0.241
p_singtor_nbd	0.184
p_chiral_restr	0.117
p_planar_d	0.028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6782
Nucleic Acid Atoms
Solvent Atoms	823
Heterogen Atoms	49

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
ARP	model building

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.