2HB9 | pdb_00002hb9

Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia (Inhibitor 3)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.75	281	1.8M AMMONIUM SULFATE, 0.1M HEPES PH 7.75, 1.5% V/V PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.09	α = 90
b = 104.09	β = 90
c = 98.21	γ = 120

Symmetry
Space Group	P 64 2 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	IMAGE PLATE	MAR scanner 345 mm plate		2006-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	19.51	99.6	0.059	0.054	11.2	6.7	31993	31993		2

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	1.75	1.84	99.6		0.381	0.287	2	5.7

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 1SML	1.75	19.67	31993	30361	1623	99.43	0.17081	0.1697	0.17	0.1912	0.19	RANDOM	16.876

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.232
r_dihedral_angle_4_deg	19.45
r_dihedral_angle_3_deg	13.107
r_dihedral_angle_1_deg	6.281
r_scangle_it	2.994
r_scbond_it	1.854
r_angle_refined_deg	1.581
r_mcangle_it	1.158
r_mcbond_it	0.705
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.232
r_dihedral_angle_4_deg	19.45
r_dihedral_angle_3_deg	13.107
r_dihedral_angle_1_deg	6.281
r_scangle_it	2.994
r_scbond_it	1.854
r_angle_refined_deg	1.581
r_mcangle_it	1.158
r_mcbond_it	0.705
r_nbtor_refined	0.306
r_nbd_refined	0.279
r_symmetry_vdw_refined	0.194
r_metal_ion_refined	0.134
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2001
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	40

Software

Software
Software Name	Purpose
XDS	data scaling
SCALA	data scaling
CCP4	model building
REFMAC	refinement
XDS	data reduction
CCP4	phasing

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.