2QGI

The UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	100mM sodium citrate (pH6.0) and 75mM magnesium acetate. Mixed 4+4ul with protein sample, hanging drop, vapor diffusion, temperature 298K., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.37	α = 90
b = 89.928	β = 90
c = 69.572	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MAR CCD 165 mm		2006-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.043	MAX II	I911-2

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	1.65	20	99.9	0.071	16.7	6.1		93646			18.1

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	1.65	1.74	100		0.388	4.6	6.1	13554

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2NXV	1.65	12.99	93484	4687	99.97	0.16	0.159	0.184	RANDOM	19.201

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.493
r_dihedral_angle_4_deg	18.131
r_dihedral_angle_3_deg	11.838
r_dihedral_angle_1_deg	6.054
r_scangle_it	5.306
r_scbond_it	3.483
r_mcangle_it	2.15
r_angle_refined_deg	2.104
r_mcbond_it	1.514
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.493
r_dihedral_angle_4_deg	18.131
r_dihedral_angle_3_deg	11.838
r_dihedral_angle_1_deg	6.054
r_scangle_it	5.306
r_scbond_it	3.483
r_mcangle_it	2.15
r_angle_refined_deg	2.104
r_mcbond_it	1.514
r_nbtor_refined	0.311
r_chiral_restr	0.274
r_symmetry_vdw_refined	0.24
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.151
r_bond_refined_d	0.026
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4040
Nucleic Acid Atoms
Solvent Atoms	721
Heterogen Atoms	27

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.