7JID | pdb_00007jid

Crystal structure of the L780 UDP-rhamnose synthase from Acanthamoeba polyphaga mimivirus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QQR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	20% PEG-8000, 2% DMSO, 100 mM CHES, 5 mM NADP(+), 5 mM UDP-L-rhamnose, 200 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.803	α = 81.94
b = 52.989	β = 88.68
c = 70.149	γ = 66.74

Symmetry
Space Group	P 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	PIXEL	Bruker PHOTON II	helios	2019-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.45	50	99.5	0.057	13.5	4.1		110458

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.55	88.7		0.384	2.7	2.1

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	4qqr	1.45	30.3	104874	5584	95.54	0.1992	0.1978	0.21	0.2268	0.23	RANDOM	17.528

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]
0.02	-0.43	-0.18	0.73	0.04	-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.652
r_dihedral_angle_4_deg	20.018
r_dihedral_angle_3_deg	13.905
r_dihedral_angle_1_deg	6.541
r_angle_refined_deg	1.853
r_angle_other_deg	1.446
r_chiral_restr	0.181
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.652
r_dihedral_angle_4_deg	20.018
r_dihedral_angle_3_deg	13.905
r_dihedral_angle_1_deg	6.541
r_angle_refined_deg	1.853
r_angle_other_deg	1.446
r_chiral_restr	0.181
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4576
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	181

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
PHASER	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.