2A81

carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A7K	monomer of 2A7K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	PEG 6000, BICINE, pH 8, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.605	α = 90
b = 139.605	β = 90
c = 78.546	γ = 120

Symmetry
Space Group	P 63

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	mirrors	2005-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.009	SRS	PX10.1

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	3.15	47.91	99.3	0.203		5.9		15149

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	3.15	3.26		94.3	0.562		3.9

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	monomer of 2A7K	3.15	47.91	15136	798	99.23	0.194	0.194	0.192	0.232	RANDOM	45.538

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]
0.75	0.38		0.75		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.448
r_dihedral_angle_4_deg	17.216
r_dihedral_angle_3_deg	16.913
r_dihedral_angle_1_deg	5.498
r_angle_refined_deg	1.114
r_scangle_it	0.903
r_angle_other_deg	0.747
r_scbond_it	0.505
r_mcangle_it	0.307
r_symmetry_hbond_refined	0.285
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.225
r_symmetry_vdw_other	0.216
r_mcbond_it	0.182
r_nbtor_refined	0.18
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.152
r_nbtor_other	0.087
r_chiral_restr	0.059
r_mcbond_other	0.042
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5304
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	52

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction