Experiment: 2QM8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QM7	MeaB Bound to GDP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1 M Bis-Tris, pH 5.5, 0.2 M Li2SO4, and 17% PEG 3350., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.41	α = 90
b = 77.04	β = 95.55
c = 79.95	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	ADSC QUANTUM 315	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2006-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.95	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	30	99.8	0.071	23.2	6.1	78116	78116		-3	28.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	99.8		0.369	4.7	5.4	7711

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MeaB Bound to GDP	1.7	29.57	74160	74160	3925	99.53	0.177	0.177	0.175	0.208	RANDOM	22

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.659
r_dihedral_angle_1_deg	4.979
r_angle_refined_deg	1.221
r_nbtor_refined	0.298
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.175
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.081
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.659
r_dihedral_angle_1_deg	4.979
r_angle_refined_deg	1.221
r_nbtor_refined	0.298
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.175
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4704
Nucleic Acid Atoms
Solvent Atoms	872
Heterogen Atoms	20

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.