3RPE | pdb_00003rpe

1.1 Angstrom Crystal Structure of Putative Modulator of Drug Activity (MdaB) from Yersinia pestis CO92.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B3D	PDB ENTRY 2B3D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	Protein: 7.8 mg/mL, 0.5 M sodium chloride, 5 mM FAD, 0.01 M Tris, pH 8.3, Screen: PACT (A2), 0.1 M SPG buffer, pH 5.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.497	α = 90
b = 66.497	β = 90
c = 76.208	γ = 120

Symmetry
Space Group	P 32

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	MARMOSAIC 300 mm CCD	Beryllium lenses	2011-04-14	M	SINGLE WAVELENGTH

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

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	1.1	30	99.9	0.049	33	5.6	153499	153499		-3	12.1

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	1.12	100		0.517	2.95	4.5	7667

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 2B3D	1.1	28.8	145242	145242	7752	99.88	0.10047	0.10047	0.0996	0.1044	0.11737	0.1208	RANDOM	13.418

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]
6.91			6.91		-13.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.234
r_dihedral_angle_4_deg	16.461
r_dihedral_angle_3_deg	11.438
r_scangle_it	4.327
r_dihedral_angle_1_deg	4.301
r_mcbond_other	3.792
r_scbond_it	3.108
r_mcangle_it	2.222
r_rigid_bond_restr	1.759
r_mcbond_it	1.585
r_angle_refined_deg	1.547
r_angle_other_deg	1.005
r_chiral_restr	0.129
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3125
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	113

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling