3R4Z

Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) in complex with alpha-d-galactopyranose from Saccharophagus degradans 2-40

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	2.4M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.207	α = 90
b = 77.128	β = 101.95
c = 90.971	γ = 90

Symmetry
Space Group	C 1 2 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 315r		2009-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2

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	1.55	50	98.2	0.058	24	3.6		125096		-3

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	1.55	1.61	85.4		0.314	2.3

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	19.77	114630	6060	96.54	0.1646	0.16353	0.18481	RANDOM	17.147

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]
-0.46		0.48	-0.7		1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.298
r_dihedral_angle_4_deg	15.589
r_dihedral_angle_3_deg	12.589
r_dihedral_angle_1_deg	6.694
r_scangle_it	3
r_scbond_it	2.025
r_angle_refined_deg	1.27
r_mcangle_it	1.19
r_mcbond_it	0.712
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.298
r_dihedral_angle_4_deg	15.589
r_dihedral_angle_3_deg	12.589
r_dihedral_angle_1_deg	6.694
r_scangle_it	3
r_scbond_it	2.025
r_angle_refined_deg	1.27
r_mcangle_it	1.19
r_mcbond_it	0.712
r_nbtor_refined	0.31
r_nbd_refined	0.192
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.133
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5744
Nucleic Acid Atoms
Solvent Atoms	693
Heterogen Atoms	24

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.