8K0O | pdb_00008k0o

High resolution structure of Dehydroascorbate Reductase from Cenchrus Americanus in complex with Acetate in the G-site and Glycerol in the H-site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EVO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	100mM SODIUM ACETATE TRIHYDRATE pH 4.6, 2M AMMONIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.389	α = 90
b = 70.389	β = 90
c = 111.69	γ = 90

Symmetry
Space Group	P 43 2 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	PIXEL	DECTRIS PILATUS3 2M		2020-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	19.85	99.8	0.997	13.4	6.7		26638

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.801	1.833	99.1		0.808	2	6.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.81	19.24	24837	1223	99.73	0.18489	0.18319	0.19	0.21888	0.22	RANDOM	38.734

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]
-0.26			-0.26		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.221
r_long_range_B_refined	7.243
r_long_range_B_other	7.106
r_dihedral_angle_1_deg	5.695
r_scangle_other	5.243
r_scbond_other	3.677
r_scbond_it	3.673
r_mcangle_other	3.329
r_mcangle_it	3.326
r_mcbond_it	2.574

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.221
r_long_range_B_refined	7.243
r_long_range_B_other	7.106
r_dihedral_angle_1_deg	5.695
r_scangle_other	5.243
r_scbond_other	3.677
r_scbond_it	3.673
r_mcangle_other	3.329
r_mcangle_it	3.326
r_mcbond_it	2.574
r_mcbond_other	2.556
r_angle_refined_deg	1.39
r_angle_other_deg	0.514
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1641
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PDB-REDO	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

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.