1M74 | pdb_00001m74

Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M6N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	299	5 mM ADP, 5 mM MgCl, 2 M ammonium sulfate, 30% glycerol, 1 mM DTT, 100 mM BES, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 299K

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.245	α = 90
b = 131.245	β = 90
c = 150.453	γ = 120

Symmetry
Space Group	P 31 1 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	AREA DETECTOR	MARRESEARCH		1997-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID2	0.986	ESRF	ID2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3	50	99.8	0.074	0.074	20.6	7.2	29711	29652		-3	58.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	99.8		1.38		1484

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	FOURIER SYNTHESIS	THROUGHOUT	1M6N	3	49.45	2	22730	1105	76.1	0.217	0.217	0.23	0.291	0.31	RANDOM	106.3

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]
-6.77	4.05		-6.77		13.54

RMS Deviations
Key	Refinement Restraint Deviation
c_scbond_it	45.42
c_scangle_it	44.27
c_dihedral_angle_d	22.9
c_mcangle_it	11.7
c_mcbond_it	7.73
c_angle_deg	1.8
c_improper_angle_d	1.68
c_bond_d	0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6402
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	53

Software

Software
Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling