2EKG

Structure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	100MM MGCL2, 100MM IMIDAZOLE PH=7.0, 14% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.383	α = 90
b = 90.104	β = 90
c = 94.83	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	173	CCD	NOIR-1	beamline optics	2007-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.0	ALS	4.2.2

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	1.9	41.96	99.3	0.059	0.059	12.5	5.82		55959			28.3

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	1.9	1.97	100		0.356	3.3	5.78	5556

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 2G37	1.9	41.1	55878	2817	99.26	0.196	0.195	0.222	RANDOM	32.299

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]
0.18			-1.28		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.829
r_dihedral_angle_4_deg	15.839
r_dihedral_angle_3_deg	14.158
r_dihedral_angle_1_deg	4.913
r_scangle_it	3.093
r_scbond_it	1.909
r_angle_refined_deg	1.314
r_mcangle_it	1.031
r_mcbond_it	0.64
r_nbtor_refined	0.304
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.087
r_symmetry_hbond_refined	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4750
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	138

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
d*TREK	data reduction