3R4Y | pdb_00003r4y

Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) 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
2.6	52.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.87	α = 90
b = 76.81	β = 101.86
c = 90.11	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		2009-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9784	ALS	5.0.2

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	1.98	50	98.4	0.086	25.3	3.8		55856		-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	1.98	2.05	98.1		0.46	4.1	3.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	19.69	50502	2710	100	0.164	0.161	0.16	0.206	0.21	RANDOM	23.83

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]
-0.06		-0.03	-0.01		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.977
r_dihedral_angle_4_deg	19.759
r_dihedral_angle_3_deg	16.801
r_dihedral_angle_1_deg	7.416
r_scangle_it	4.725
r_scbond_it	3.112
r_mcangle_it	1.977
r_angle_refined_deg	1.627
r_mcbond_it	1.226
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.977
r_dihedral_angle_4_deg	19.759
r_dihedral_angle_3_deg	16.801
r_dihedral_angle_1_deg	7.416
r_scangle_it	4.725
r_scbond_it	3.112
r_mcangle_it	1.977
r_angle_refined_deg	1.627
r_mcbond_it	1.226
r_nbtor_refined	0.318
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.119
r_symmetry_hbond_refined	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5755
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	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.