3G32 | pdb_00003g32

CTX-M-9 class A beta-lactamase complexed with compound 6 (3G3)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	292	Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.11	α = 90
b = 107.098	β = 101.66
c = 47.477	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM Q315r	mirrors	2008-04-11		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.31	50	99.4	0.058		3.9		104746		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.31	1.36	98.3		0.315		3.7	10346

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 (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 1YLJ	1.31	44.19	104717	5239	99.27	0.154	0.152	0.15	0.182	0.18	RANDOM	14.128

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]
-0.06		0.51	-0.06		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.745
r_dihedral_angle_3_deg	11.699
r_dihedral_angle_4_deg	11.618
r_dihedral_angle_1_deg	5.718
r_sphericity_free	2.315
r_scangle_it	2.154
r_sphericity_bonded	1.784
r_scbond_it	1.454
r_angle_refined_deg	1.393
r_mcangle_it	1.021
r_rigid_bond_restr	0.753
r_mcbond_it	0.646
r_nbtor_refined	0.299
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.096
r_symmetry_hbond_refined	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4064
Nucleic Acid Atoms
Solvent Atoms	677
Heterogen Atoms	83

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing