7QOR | pdb_00007qor

Structure of beta-lactamase TEM-171

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3JYI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG-4000, 0.2 M calcium acetate, 0.1 M Tris-HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.19	α = 90
b = 88.19	β = 90
c = 499.323	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976300	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.999	86.85	98.6	0.99	18.5	13.2		132474

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.999	2.05			0.787

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3JYI	1.999	15	132051	6526	97.834	0.191	0.1899	0.2	0.2106	0.21	58.018

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]
1.363			1.363		-2.727

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.463
r_dihedral_angle_4_deg	15.345
r_dihedral_angle_3_deg	13.932
r_lrange_it	7.314
r_lrange_other	7.257
r_dihedral_angle_1_deg	6.406
r_scangle_it	2.418
r_scangle_other	2.418
r_mcangle_it	1.901
r_mcangle_other	1.901
r_angle_refined_deg	1.558
r_scbond_it	1.448
r_scbond_other	1.448
r_angle_other_deg	1.356
r_mcbond_it	1.17
r_mcbond_other	1.17
r_nbd_other	0.229
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_refined	0.195
r_symmetry_nbd_other	0.185
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.153
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12168
Nucleic Acid Atoms
Solvent Atoms	875
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing