3H5N | pdb_00003h5n

Crystal structure of E. coli MccB + ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H5A	PDB entry 3H5A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291.2	24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 25 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.847	α = 90
b = 138.239	β = 92.62
c = 80.224	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	IMAGE PLATE	MAR scanner 300 mm plate	Rosenbaum-Rock vertical focusing mirror	2007-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97926	APS	22-ID

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	1.85	50	92.9	0.054	19.166	3.1	96263	96263			24.9

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)
	1.85	1.92	89		0.364		2.8	9202

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	PDB entry 3H5A	1.9	42.64	88775	4421	93.01	0.207	0.204	0.2041	0.256	0.2569	RANDOM	22.839

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]
0.28		-0.15	-0.43		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.707
r_dihedral_angle_4_deg	21.183
r_dihedral_angle_3_deg	15.052
r_dihedral_angle_1_deg	6.15
r_scangle_it	2.852
r_scbond_it	2.021
r_angle_refined_deg	1.323
r_mcangle_it	1.129
r_mcbond_it	0.909
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.253
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.091
r_metal_ion_refined	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10428
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	137

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