4LC1 | pdb_00004lc1

MeaB, A Bacterial Homolog of MMAA, Bound to GDP and crystallized in the presence of GDP and [AlF4]-

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QM7	PDB ENTRY 2QM7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20 % (w/v) PEG3350, and 0.2 M sodium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.667	α = 90
b = 78.623	β = 108.61
c = 69.622	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 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2008-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03262	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	99.5			60395	60064

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.91	97.7		0.393	0.403	4.43	4.2	9832

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 2QM7	1.8	47.89	60227	57038	3026	99.73	0.196	0.18127	0.17934	0.19	0.21652	0.23	RANDOM	27.253

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]
0.65		0.48	-1.38		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.787
r_dihedral_angle_4_deg	16.995
r_dihedral_angle_3_deg	12.887
r_dihedral_angle_1_deg	5.312
r_angle_other_deg	2.981
r_angle_refined_deg	1.483
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.787
r_dihedral_angle_4_deg	16.995
r_dihedral_angle_3_deg	12.887
r_dihedral_angle_1_deg	5.312
r_angle_other_deg	2.981
r_angle_refined_deg	1.483
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4613
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	62

Software

Software
Software Name	Purpose
Blu-Ice	data collection
EPMR	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.