3H5R

Crystal structure of E. coli MccB + Succinimide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H5N	PDB entry 3H5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.2	24-26% pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Bis-Tris pH 6.5, 50 mM (NH4)2SO4, 10 mM Succinimidyl peptide, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.934	α = 90
b = 137.972	β = 92.1
c = 80.134	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	CCD	MARMOSAIC 225 mm CCD	Sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2008-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00000	APS	22-BM

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	2.1	50	99.9	0.09	22.181	4.4	71440	71440			37

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	2.1	2.18	99.9		0.546		4.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3H5N	2.1	27.95	70567	3553	99.88	0.19658	0.19375	0.24995	RANDOM	45.108

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]
1		-0.35	-1.33		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.757
r_dihedral_angle_4_deg	19.005
r_dihedral_angle_3_deg	17.778
r_dihedral_angle_1_deg	6.405
r_scangle_it	3.252
r_scbond_it	2.247
r_angle_refined_deg	1.518
r_mcangle_it	1.378
r_mcbond_it	0.92
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.183
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.11
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10435
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
X-GEN	data scaling
HKL-2000	data reduction
REFMAC	phasing