9G99 | pdb_00009g99

Joint neutron and x-ray structure of apo alginate lyase PsAlg7C

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8C3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30% PEG3350,0.1M Bis-Tris pH 5.5, 0.3M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.577	α = 90
b = 60.971	β = 90
c = 91.308	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	neutron	293	SCINTILLATION	ORNL ANGER CAMERA		2021-06-01	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M		2021-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2-4	ORNL Spallation Neutron Source	MANDI
2	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	2.15	13.85	84.4	0.19			0.11	0.9		5.29	3.2		11082
2	1.8	27.23	99.92	0.13			0.037	0.98		20.7	12.6		22174

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.23		0.23			0.14	0.45		3.48
2	1.8	1.86		0.44			0.14	0.94		6.08

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.15	13.85				11081	549	84.45		0.235	0.232		0.302			20.04
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.8	27.23				22174	2082	99.97		0.123	0.121	0.3191	0.164	0.3254		20.04

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
f_dihedral_angle_d	18.185

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1768
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms

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.