8J6Y

Crystal structure of class A beta-lactamase PSE-4 WT- Apo state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G68

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.951	α = 90
b = 95.951	β = 90
c = 61.509	γ = 90

Symmetry
Space Group	P 41 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	RIGAKU HyPix-6000HE	X ray Optics	2023-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.4	27.226	98.9	0.153	0.161	0.049	0.999	14.6	19.5		11708

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			1.228	1.292	0.4	0.955		19.4

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.4	27.226	11566	573	77.9944	0.213	0.2088	0.2719	42.031

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]
-2.611			-2.611		5.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.918
r_dihedral_angle_3_deg	15.207
r_dihedral_angle_2_deg	11.925
r_lrange_it	9.139
r_lrange_other	9.07
r_dihedral_angle_1_deg	7.335
r_scangle_it	6.786
r_scangle_other	6.235
r_mcangle_it	5.628
r_mcangle_other	5.626
r_scbond_it	4.703
r_scbond_other	4.149
r_mcbond_it	4.033
r_mcbond_other	4.016
r_angle_refined_deg	1.559
r_angle_other_deg	0.502
r_nbd_refined	0.232
r_symmetry_nbd_refined	0.214
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.199
r_nbtor_refined	0.182
r_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.065
r_bond_refined_d	0.007
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	2038
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data collection
Coot	model building
Aimless	data scaling
MOLREP	phasing