7OCU | pdb_00007ocu

Mannitol-1-phosphate bound to the phosphatase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD-N374A from Acinetobacter baumannii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OCN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1M BIS-Tris propane pH6.5, 0.25M Na2SO4, 18% PEG3350, 0.02M MgCl2, 0.1M potassium acetate with microseeding

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.439	α = 90
b = 157.433	β = 90
c = 219.824	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER X 9M		2019-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9801	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	48.49	100	0.115	0.119	0.032	0.999	16.4	13.9		47757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.79	100		1.914	1.984	0.52	0.831		14.3

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	THROUGHOUT	7OCN	2.7	48.49	45334	2380	99.97	0.2287	0.2268	0.23	0.2643	0.26	RANDOM	88.16

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]
-2.57			-4.34		6.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.395
r_dihedral_angle_3_deg	12.664
r_dihedral_angle_4_deg	10.658
r_dihedral_angle_1_deg	4.697
r_angle_refined_deg	1.136
r_angle_other_deg	1.019
r_chiral_restr	0.029
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.395
r_dihedral_angle_3_deg	12.664
r_dihedral_angle_4_deg	10.658
r_dihedral_angle_1_deg	4.697
r_angle_refined_deg	1.136
r_angle_other_deg	1.019
r_chiral_restr	0.029
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11018
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	54

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	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.