5F12 | pdb_00005f12

WrbA in complex with FMN under crystallization conditions of WrbA-FMN-BQ structure (4YQE)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.1 M MES/Imidazol, 12.5 % PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.75	α = 90
b = 60.75	β = 90
c = 169.02	γ = 90

Symmetry
Space Group	P 41 21 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 PILATUS 6M		2015-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	50	99.9	0.1	11.7	8.4	51772	51696

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	99.4		0.79	2.21	8.5

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	3b6i	1.5	42.96	49068	2628	99.85	0.1794	0.1779	0.1868	0.2053	0.2113	RANDOM	21.533

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
r_dihedral_angle_2_deg	34.081
r_dihedral_angle_3_deg	11.774
r_dihedral_angle_4_deg	11.37
r_dihedral_angle_1_deg	6.943
r_angle_refined_deg	2.004
r_angle_other_deg	1.388
r_chiral_restr	0.125
r_bond_refined_d	0.02
r_gen_planes_refined	0.016
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2811
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	62

Software

Software
Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
BALBES	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling