4LOC

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxamate and biotin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JX4	PDB ENTRY 4JX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH CRYSTALLIZATION UNDER OIL	6	298	14% (w/v) PEG 8000, 110 mM MOPS (pH 6.0), 165 mM Tetramethylammonium chloride, 2% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.87	α = 90
b = 157.123	β = 90
c = 244.714	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2011-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.26	50	98.3	0.084	20.6	7.1	148360	145868		-3	34.4

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)
1	2.26	2.3	94.7		0.444	3.4	6.8

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 4JX4	2.26	43.75	140726	7444	97.97	0.17837	0.17635	0.21628	RANDOM	50.934

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]
4.52			-1.78		-2.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.428
r_dihedral_angle_4_deg	19.813
r_dihedral_angle_3_deg	15.782
r_dihedral_angle_1_deg	6.359
r_long_range_B_refined	5.794
r_long_range_B_other	5.794
r_scangle_other	2.931
r_mcangle_it	2.462
r_mcangle_other	2.462
r_scbond_it	2.241
r_scbond_other	2.241
r_angle_refined_deg	1.836
r_mcbond_it	1.656
r_mcbond_other	1.655
r_angle_other_deg	0.896
r_chiral_restr	0.1
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17888
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	111

Software

Software
Software Name	Purpose
MD2	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling