2QF7 | pdb_00002qf7

Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5.6	298	7.5 mg/mL PC, 2.5 mM ATP-gamma-S, 1 mM ethyl CoA, 280 mM sodium formate, 70 mM sodium acetate, 60 mM calcium chloride, 5.9% PEG 8K, pH 5.6, EVAPORATION, temperature 298K
2	VAPOR DIFFUSION, HANGING DROP	5.6	298	400 mM sodium formate, 80 mM sodium acetate, 80 mM calcium chloride, 14 mM 3-(N,N-Dimethyltetradecylammonio)propanesulfonate, 9% PEG 8K, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.729	α = 90
b = 93.258	β = 107.33
c = 137.222	γ = 90

Symmetry
Space Group	C 1 2 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	SBC-3		2006-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97907	APS	19-BM

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	2	30	96.7	0.057	20.1	4	184567	184296			25.8

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	2	2.07	86		0.321	3.1	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2	131.31	184296	9277	96.92	0.18	0.178	0.1781	0.223	0.2217	RANDOM	25.599

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]
-0.99		-0.86	-0.7		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_4_deg	18.306
r_dihedral_angle_3_deg	14.836
r_dihedral_angle_1_deg	6.761
r_scangle_it	3.187
r_scbond_it	2.205
r_angle_refined_deg	1.623
r_mcangle_it	1.351
r_mcbond_it	0.893
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_4_deg	18.306
r_dihedral_angle_3_deg	14.836
r_dihedral_angle_1_deg	6.761
r_scangle_it	3.187
r_scbond_it	2.205
r_angle_refined_deg	1.623
r_mcangle_it	1.351
r_mcbond_it	0.893
r_nbtor_refined	0.308
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.201
r_metal_ion_refined	0.198
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.121
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15782
Nucleic Acid Atoms
Solvent Atoms	1318
Heterogen Atoms	118

Software

Software
Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	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.