4DGT | pdb_00004dgt

Crystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630 crystallized with magnesium formate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T32	SwissModel generated model based on PDB ENTRY 3T32 structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	25% PEG 3350, 2M Mg Formate, pH 7.0, vapor diffusion, hanging drop, temperature 20K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.744	α = 90
b = 55.624	β = 91.25
c = 79.133	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210r	mirrors	2011-07-06		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.55	50	99.5	0.074	0.074	19	3.6	99598	99100		-3	13

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	94.1		0.407	0.407	2.3	2.5	4608

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SwissModel generated model based on PDB ENTRY 3T32 structure	1.55	50	99489	99012	4947	99.52	0.1491	0.1491	0.1475	0.16	0.1809	0.19	RANDOM	17.2009

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]
-0.04		0.08	-0.33		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.168
r_dihedral_angle_3_deg	13.837
r_dihedral_angle_4_deg	10.781
r_dihedral_angle_1_deg	5.998
r_angle_other_deg	2.428
r_angle_refined_deg	1.817
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.168
r_dihedral_angle_3_deg	13.837
r_dihedral_angle_4_deg	10.781
r_dihedral_angle_1_deg	5.998
r_angle_other_deg	2.428
r_angle_refined_deg	1.817
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6274
Nucleic Acid Atoms
Solvent Atoms	878
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
CCP4	phasing

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.