8JK3 | pdb_00008jk3

Crystal Structure of Bel-1 Extended Spectrum Beta-lactamase in Hexagonal Form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EOE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium pH 7.5, 30% v/v 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.192	α = 90
b = 121.192	β = 90
c = 72.128	γ = 120

Symmetry
Space Group	P 65

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	RIGAKU HyPix-6000HE	X ray optics	2022-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.5	29.126	99.9	0.99	18.4	7.6		96340

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	1.5	8.22			0.418

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.5	29.126	96119	4975	99.751	0.153	0.15	0.15	0.2088	0.21	20.523

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]
-0.048	-0.024		-0.048		0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.773
r_dihedral_angle_3_deg	13.635
r_dihedral_angle_2_deg	9.008
r_dihedral_angle_1_deg	6.103
r_rigid_bond_restr	5.93
r_lrange_it	4.403
r_lrange_other	4.398
r_scangle_it	3.476
r_scangle_other	3.476
r_scbond_it	2.702
r_scbond_other	2.702
r_mcangle_other	2.532
r_mcangle_it	2.526
r_mcbond_it	2.018
r_angle_refined_deg	2.009
r_mcbond_other	2.003
r_angle_other_deg	0.675
r_metal_ion_refined	0.454
r_symmetry_xyhbond_nbd_refined	0.275
r_symmetry_nbd_refined	0.255
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.227
r_nbd_other	0.209
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.183
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4063
Nucleic Acid Atoms
Solvent Atoms	608
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing