4R3B | pdb_00004r3b

Crystal structure of SHV-1 b-lactamase in complex with 6b-(hydroxymethyl)penicillanic acid sulfone PSR-283A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	21-30% PEG6000, 0.1M HEPES pH 6.2-8.2, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.238	α = 90
b = 55.274	β = 90
c = 84.465	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	CCD	MARMOSAIC 325 mm CCD		2010-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.366	50	98.6	0.035	28.3	3.5	46988	46331	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.366	1.42	94.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.366	27.73	46331	2470	98.48	0.13242	0.13032	0.13	0.17213	0.17	RANDOM	16.951

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]
0.07			0.01		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.735
r_sphericity_free	22.022
r_dihedral_angle_4_deg	20.16
r_dihedral_angle_3_deg	13.431
r_scangle_it	12.557
r_sphericity_bonded	11.366
r_scbond_it	9.864
r_dihedral_angle_1_deg	5.94
r_rigid_bond_restr	5.896
r_mcangle_it	5.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.735
r_sphericity_free	22.022
r_dihedral_angle_4_deg	20.16
r_dihedral_angle_3_deg	13.431
r_scangle_it	12.557
r_sphericity_bonded	11.366
r_scbond_it	9.864
r_dihedral_angle_1_deg	5.94
r_rigid_bond_restr	5.896
r_mcangle_it	5.624
r_mcbond_it	4.468
r_angle_refined_deg	1.359
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2024
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	61

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.