2GJ9 | pdb_00002gj9

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	16-19% PEG 3350, 100 mM MES pH 6.0, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.24	α = 90
b = 70.1	β = 95.76
c = 90.21	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		CCD	MARMOSAIC 225 mm CCD		2005-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.815	SLS	X10SA

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	20	96.3	0.069	8.61			48094			29.19

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)
	2	2.1		87.5	0.228	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	20	47813	47813	2446	99.42	0.252	0.252	0.25	0.252	0.299	0.3014	RANDOM	25.14

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]
-0.82		0.06	1.19		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.505
r_dihedral_angle_3_deg	19.004
r_dihedral_angle_4_deg	18.174
r_dihedral_angle_1_deg	6.893
r_scangle_it	4.399
r_scbond_it	2.819
r_angle_refined_deg	1.86
r_mcangle_it	1.772
r_mcbond_it	1.058
r_nbtor_refined	0.305
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.231
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.122
r_metal_ion_refined	0.115
r_symmetry_hbond_refined	0.102
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4888
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	140

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing