4AM8

Crystal structure of the R54G mutant of putrescine transcarbamylase from Enterococcus faecalis bound to a curing guanidinium ion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A8P	PDB ENTRY 4A8P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.02 M MAGNESIUM CHLORIDE, 30 % PEG 550 MONOMETHYLETHER, 0.1 M HEPES PH 7.5, 0.001 M PALO, 0.05 M GUANIDINIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.35	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.69	α = 90
b = 130.6	β = 104.25
c = 164.157	γ = 90

Symmetry
Space Group	I 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	100	CCD	MARMOSAIC 225 mm CCD		2010-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	1.99	41	90	0.07	8.6	3.8		130385		2

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	30	82		0.34	2	3.5

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 4A8P	1.99	25	123626	6567	89.77	0.18335	0.18215	0.20571	RANDOM	25.913

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]
0.23		-0.13	-0.41		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.554
r_dihedral_angle_4_deg	16.196
r_dihedral_angle_3_deg	11.595
r_dihedral_angle_1_deg	5.083
r_angle_other_deg	1.112
r_angle_refined_deg	1.108
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15543
Nucleic Acid Atoms
Solvent Atoms	825
Heterogen Atoms	178

Software

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