5TOY | pdb_00005toy

X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with CTX-M-14 E166A Beta-Lactamase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XXR	PDB Entry 4XXR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	293.15	potassium phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.012	α = 90
b = 106.787	β = 101.76
c = 47.759	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	RAYONIX MX300-HS		2014-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.3	53.39	100	0.095	15.8	3.4		103057

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	1.3	1.32	100		2.9	2.7

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 4XXR	1.3	53.39	103057	5418	99.78	0.14354	0.1425	0.14	0.16325	0.16	RANDOM	15.086

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]
-0.2		1.41	-0.89		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.348
r_sphericity_free	14.394
r_dihedral_angle_3_deg	14.359
r_dihedral_angle_4_deg	11.781
r_dihedral_angle_1_deg	7.068
r_sphericity_bonded	4.583
r_rigid_bond_restr	1.614
r_angle_refined_deg	1.472
r_long_range_B_refined	1.038
r_long_range_B_other	1.038
r_angle_other_deg	0.696
r_mcangle_it	0.223
r_mcangle_other	0.223
r_scangle_other	0.186
r_mcbond_it	0.147
r_mcbond_other	0.147
r_scbond_it	0.123
r_scbond_other	0.123
r_chiral_restr	0.093
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3899
Nucleic Acid Atoms
Solvent Atoms	600
Heterogen Atoms	214

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing