3DTM | pdb_00003dtm

Increased folding stability of TEM-1 beta-lactamase by in-vitro selection

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BTL	PDB ENTRY 1BTL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288	1.6-1.8 M Ammonium citrate, 5% PEG 400, 0.1M Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.82	α = 90
b = 79.68	β = 90
c = 87.07	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	IMAGE PLATE	MAR scanner 345 mm plate		2006-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	19.59	99.75			23406	23406	5	8.3

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)
	1.86	1.9	97.6		0.348	0.348	3.6

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 (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	PDB ENTRY 1BTL	2	19.41	18342	18342	991	99.75	0.21785	0.215	0.22	0.27163	0.23	RANDOM	6.495

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]
0.03			0.01		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.34
r_dihedral_angle_4_deg	19.544
r_dihedral_angle_3_deg	16.645
r_dihedral_angle_1_deg	5.757
r_scangle_it	2.773
r_scbond_it	1.67
r_angle_refined_deg	1.361
r_mcangle_it	1.006
r_mcbond_it	0.606
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.231
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2021
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
XDS	data reduction
ADDREF	data scaling
AMoRE	phasing