4JX6 | pdb_00004jx6

Structure of the carboxyl transferase domain Y628A from Rhizobium etli pyruvate carboxylase with pyruvate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QF7	CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	298	11.7% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 200 mM Tetramethylammonium chloride, 3% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.809	α = 90
b = 157.28	β = 90
c = 245.885	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 300 mm CCD		2012-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.78	50	99.9	0.074	26.3	7.2	83991	83911		-3

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	2.78	2.83	99.6		0.426	4.3	7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7	2.78	50	79718	4189	99.8	0.21147	0.20894	0.21	0.25844	0.26	RANDOM	72.618

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]
8.91			-2.29		-6.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.986
r_dihedral_angle_4_deg	20.071
r_dihedral_angle_3_deg	17.043
r_dihedral_angle_1_deg	5.908
r_angle_refined_deg	1.384
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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	17245
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	26

Software

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