Experiment: 7L2A

Molybdopterin cofactor biosynthesis protein E from Burkholderia multivorans ATCC 17616

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QIE	PDB entry 2QIE as per MoRDa

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	287	Molecular Dimensions Morpheus screen, E3: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M MES/imidazole pH 6.5: BumuA.00098.a.B1.PS37859 at 41.7mg/ml + 0.5% beta-octyl-glucoside: cryo: direct: tray 317330e3, puck xxu3-3.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.73	α = 90
b = 72.66	β = 90
c = 105.77	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	x-ray	100	CCD	RAYONIX MX-300	Beryllium Lenses	2020-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	50	99.9	0.042	0.045	0.999	23.12	6.821		32130			39.047

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	99.5		0.407	0.465	0.946	2.88	4.241

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	PDB entry 2QIE as per MoRDa	1.85	42.76	1.36	32104	2018	99.86	0.191	0.1887	0.1888	0.2232	0.2231	0	45.93

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	12.0241
f_angle_d	0.9393
f_chiral_restr	0.0641
f_plane_restr	0.0091
f_bond_d	0.0078

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2219
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	21

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building