7A10 | pdb_00007a10

LppS with covalent adduct derived from 1g

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.25	293	Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K The crystals were cryo-protected by dipping them in mother liquor with increased 25% PEG 6K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.23	α = 90
b = 89.806	β = 103.96
c = 67.005	γ = 90

Symmetry
Space Group	P 1 21 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	DECTRIS EIGER X 16M	mirrors (VFM, HFM)	2019-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.82656	MAX IV	BioMAX

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	1.85	39.44	96.5	0.084	0.099	0.053	0.999	11.7	6.5		42829		1.2	19.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	75.4		1.047	0.847	0.548	1.2	4.4

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	5LBG	1.85	39	40691	2110	96.45	0.1887	0.1869	0.194	0.2239	0.2342	RANDOM	33.308

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]
0.36		0.01	1.24		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.786
r_dihedral_angle_4_deg	17.071
r_dihedral_angle_3_deg	14.153
r_dihedral_angle_1_deg	5.581
r_angle_refined_deg	1.864
r_angle_other_deg	1.058
r_chiral_restr	0.116
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3976
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	18

Software

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