4DE2 | pdb_00004de2

CTX-M-9 class A beta-lactamase complexed with compound 12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G35	pdb entry 3G35

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	Potassium Phosphate, pH 8.5, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.125	α = 90
b = 106.922	β = 101.47
c = 47.481	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 210	mirrors	2010-06-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9795	NSLS	X6A

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	1.4	50	99.7	0.07	14.8	3.7	86492	86200		5

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	1.4	1.42	95.2		0.539		3.2	4056

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 3G35	1.4	50	86492	86107	4313	99.54	0.1561	0.1541	0.1466	0.1938	0.1854	RANDOM	12.9194

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]
-0.01		1.87	-0.67		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.511
r_dihedral_angle_3_deg	12.23
r_dihedral_angle_4_deg	11.51
r_dihedral_angle_1_deg	5.779
r_scangle_it	4.136
r_scbond_it	2.747
r_mcangle_it	1.684
r_rigid_bond_restr	1.191
r_angle_refined_deg	1.149
r_mcbond_it	1.082
r_chiral_restr	0.087
r_gen_planes_refined	0.012
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3888
Nucleic Acid Atoms
Solvent Atoms	546
Heterogen Atoms	104

Software

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